Software/list

Below is (one of many possible) dynamic tables of software data, created from pages in the wiki. To add a package to the list, use the following form:

 

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Name	Summary	Bio Tags	Meth Tags	Features	Language	Licence	OS
.NET BIO	".NET Bio is an open source library of common bioinformatics functions, intended to simplify the creation of life science applications. The core library implements a range of file parsers and formatters for common file types, connectors to commonly-used web services such as NCBI BLAST, and standard algorithms for the comparison and assembly of DNA, RNA and protein sequences. Sample tools and code snippets are also included."	Sequence analysis			C#		Windows Linux
4peaks	Allows viewing sequencing trace files, motif searching trimming, BLAST and exporting sequences.	Sequencing	Sequence analysis			Freeware	Mac OS X
A5	A5 is an integrative pipeline for genome assembly that automates sequence data cleaning, error correction, assembly, and quality control by chaining a number of programs together with additional custom algorithms.	Sequence assembly	De-novo assembly			GPLv3	Linux Mac OS X
AB Large Indel Tool	Identifies deviations in clone insert size that indicate intra-chromosomal structural variations compared to a reference genome.	Indel detection Sequencing	Mapping		Perl	GPL	Linux 64
AB Small Indel Tool	The SOLiD™ Small Indel Tool processes the indel evidences found in the pairing step of the SOLiD™ System Analysis pipeline Tool (Corona Lite).	Indel detection Sequencing	Read mapping Sequence alignment		Perl C++	GPL	Linux 64
ABBA	Assembly Boosted By Amino acid sequence is a comparative gene assembler, which uses amino acid sequences from predicted proteins to help build a better assembly	Sequence assembly	Sequence assembly Scaffolding			Artistic License	Linux
ABMapper	Maps RNA-Seq reads to target genome considering possible multiple mapping locations and splice junctions	Genomics Transcriptomics	Read mapping Sequence alignment		C++ Perl	GPLv3	Linux
ABySS	ABySS is a de novo sequence assembler designed for short reads and large genomes.	Sequence assembly (de novo assembly)	Sequence assembly Sequence assembly (de-novo assembly)	MPI OpenMP	C++	Commercial Freeware	POSIX Linux Mac OS X
Adapter Removal (software)	Removes adaptor fragments from raw short read sequence data and outputs data to FASTA format.	Workflows	Adapter removal	Sequence trimming	Java	Custom Licence	Linux 64 Windows Mac OS X
ADTEx	Aberration Detection in Tumour Exome (ADTEx) is a tool for copy number variation (CNV) detection for whole-exome data from paired tumour/matched normal samples.	Copy number estimation Exome analysis Cancer biology Next Generation Sequencing	Statistical calculation	Copy number analysis	Python R	GPLv3	GNU/Linux
AGE	AGE is a tool that implements an algorithm for optimal alignment of sequences with SVs.	Structural variation	Sequence alignment			Creative Commons license (Attribution-NonCommerical).
AGILE	A hash table based high throughput sequence mapping algorithm for longer 4A54 reads that uses diagonal multiple seed-match criteria, customized q-gram filtering and a dynamic incremental search approach among other heuristics to optimize every step of the mapping process		Mapping		C
Agp2amos	missing		Formatting				Windows Linux
Alcovna	ALgorithms for COmparing and Visualizing Non Assembled data	SNP detection			Java
ALEXA-Seq	Alternative Expression Analysis by massively parallel RNA sequencing	RNA-Seq quantification Alternative splicing			Perl	GPLv3
ALLPATHS	De novo assembly of whole-genome shotgun microreads.	Sequence assembly (de novo assembly)	Sequence assembly Sequence assembly (de-novo assembly)
Alta-Cyclic	Alta-Cyclic is a Illumina Genome-Analyzer (Solexa) base caller.		Base-calling
AMOS	AMOS is a Modular, Open-Source whole genome assembler.		Sequence assembly Sequence assembly validation Integrated solution Formatting Sequence assembly visualisation		C Perl		Linux
ANCHOR	Post-processing tools for de novo assemblies	De-novo assembly	Sequence assembly		C++ Python	BCCA (academic use)	Linux
AnCorr	Webserver/tool for evaluation coordinate and ordinal correlations between genomic tracks and/or expression or protein binding profiles.	Genomics	Statistical calculation Correlation	Easy-to-use point-and-click web interface with context help	Perl C CGI PHP JavaScript	free for non-commercial academic research	Cross-Platform
Anno-J	Annotation Browsing 2.0	Sequencing	Visualisation			Creative Commons - Attribution-NonCommercial-ShareAlike
ANNOVAR	ANNOVAR: Functional annotation of genetic variants from high-throughput sequencing data	Genomics Genetics	Annotation Variant prioritisation	Gene-based annotation region-based annotation filter-based annotation	Perl	Commercial Freeware	Linux Windows Mac OS X
Arachne	ARACHNE is a program for assembling data from whole genome shotgun sequencing experiments.		Sequence assembly
AREM	AREM: Aligning Short Reads from ChIP-sequencing by Expectation Maximisation	ChIP-seq	Read mapping Peak calling		Python		Linux
Arf	arf is a genetic analysis program for sequencing data.
Array Suite (Array Studio/Server)	Array Studio is a complete analysis and visualization package for NextGen sequencing data, as well as other -OMIC data types. Array Server is a backend enterprise server for storage and analysis of -OMIC and NextGen sequencing data.	Genomics SNP detection Indel detection	Read mapping Gene expression profiling	Data Visualisation Variant annotation and analysis coverage analysis Read mapping	C#	Commercial	Windows
ArrayExpressHTS	R-based pipeline for RNA-Seq data analysis.	RNA-Seq RNA-Seq quantification			R
ArrayStar	ArrayStar is an easy-to-use gene expression analysis software package that offers powerful visualization and statistical tools to help you analyze your microarray data.	Gene expression analysis	Statistical calculation Differential expression analysis Ontology comparison Genetic variation analysis			Commercial	Windows 7 64-bit or Higher Mac OS X 10.7 10.8 or 10.9 with Parallels Desktop
ASC	Empirical Bayes method to detect differential expression.	RNA-Seq quantification	Statistical calculation and probability
ATAC	ATAC is a computational process for comparative mapping between two genome assemblies, or between two different genomes.		Sequence alignment Sequence assembly validation				Linux
Atlas Suite	Atlas is a suite of variant analysis tools specializing in the separation of true SNPs and insertions and deletions (indels) from sequencing and mapping errors in Whole Exome Capture Sequecing (WECS) data. SNPs may be called using the Atlas-SNP2 application and indels may be called using the Atlas-Indel2 application.	SNP detection Indel detection	Variant calling		Ruby C	BSD	POSIX
Atlas-SNP2	Atlas-SNP2 is a SNP detection tool developed for next generation sequencing platforms	SNP detection			Ruby	Freeware	UNIX
Avadis NGS	Strand NGS formerly Avadis NGS is a desktop software platform for alignment, analysis, visualization, and management of data generated by next-generation sequencing (NGS) platforms. It supports workflows for RNA-Seq, DNA-Seq, small RNA-Seq, ChIP-seq, and Methyl-Seq data analysis. Strand NGS is designed with the biologist in mind.	ChIP-seq RNA-Seq Sequencing DNA-Seq Small RNA-Seq RNA Methyl-Seq MeDIP-Seq Pathway or network analysis	Sequence alignment Visualisation Sequencing quality control Sequence analysis Analysis Biological interpretation	Rich Visualisation Identify effects of SNPs on transcripts Identify Structural Variants from Paired Reads (Insertions Deletions Translocations Inversions) Identify binding site peaks in ChIP-seq data Identify motifs around binding sites Determine gene expression levels and identify differentially expressed genes De-convolve transcript expression levels and identify differential splice variants Identify Novel Exons Identify Novel Splice Junctions Identify Fusion Genes Perform QC on Reads determine on-and off-target reads and filter anomalous reads Determine Enriched GO Terms Determine Significant Pathways	Java R Python	Commercial	Windows Linux Mac OS X
Baa.pl	use transcripts to assess a de novo assembly	Sequence assembly (de novo assembly)	Sequence assembly validation Sequence alignment analysis		Perl	GPL	any
Bambino	Variant detector and graphical alignment viewer for SAM/BAM format data.	SNP detection Genetic variation			Java
Bambus	Bambus is a general purpose scaffolder		Scaffolding
BAMseek	BAMseek is a large file viewer for BAM and SAM alignment files.	Genomics Transcriptomics	Sequence alignment visualisation		Java	GPLv3	Cross-Platform
BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.		Sequence alignment analysis		C++	MIT	Cross-Platform
BamView	Interactive Java application for visualising the large amounts of data stored for sequence reads which are aligned against a reference genome sequence		Visualisation		Java	GPL	Mac OS X UNIX Windows
Barcode generator	Generator of sequence barcodes suitable for Illumina sequencing.		DNA barcoding		Python
Barcrawl Bartab	Barcrawl facilitates the design of barcoded primers, for multiplexed high-throughput sequencing.		DNA barcoding			GPL
BarraCUDA	Barracuda is a high-speed sequence aligner based on BWA and uses the latest Nvidia CUDA architecture for accelerating alignments of sequence reads generated by the next-generation sequencers.	Sequence analysis	Read mapping Sequence alignment	Gapped and ungapped alignment paired-end mapping GPGPU parallel execution	C C++ CUDA	GPLv3 MIT	Linux
Batman	Bayesian tool for methylation analysis (Batman) for analyzing methylated DNA immunoprecipitation (MeDIP) profiles	DNA methylation			Java	LGPL
BayesCall	Bayesian basecaller	Sequencing	Base-calling		C++ Python	GPLv3
BayesPeak	A Bayesian hidden Markov model to detect enriched locations in ChIP-seq data.	ChIP-seq Simulation experiment	Statistical calculation	Multicore	R	GPL
BaySeq	Identify differential expressed genes	RNA-Seq quantification	Differential expression analysis		R
BBMap	BBMap is a fast splice-aware aligner for RNA and DNA. It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels.	Sequence alignment Whole genome resequencing RNA-Seq alignment SNP detection Metagenomics Phylogenetics Alternative splicing Resequencing Quality control Read binning	Read mapping Sequence alignment Sequence contamination filtering Sequence trimming RNA-Seq analysis	Multithreaded. Faster and more accurate than competing aligners. Splice-aware.	Java 7	BSD	Windows NIX Mac OS X all supporting JVM
BBSeq	Tool for analyzing RNA-Seq data to analyze gene expression	RNA-Seq quantification			R
Bcbio-nextgen	Python scripts and modules for automated next gen sequencing analysis. These provide a fully automated pipeline for taking sequencing results from an Illumina sequencer, converting them to standard Fastq format, aligning to a reference genome, doing SNP calling, and producing a summary PDF of results.	Workflows	Read mapping Sequence alignment Peak calling Sequence motif recognition Genotyping Sequencing quality control Differential expression analysis Sequence trimming Filtering Genomic region matching		Python	MIT	platform-independent
BEADS	ChIP-seq data normalization for Illumina	ChIP-seq	Standardisation and normalisation
BEAP	The Blast Extension and Assembly Program (BEAP) uses a short starting DNA fragment to recursively blast nucleotide databases to obtain all sequences that overlaps to construct the a "full length" sequence.		Read mapping
BEDTools	BEDTools is an extensive suite of utilities for comparing genomic features in BED format.	Genomics	Mapping	Feature overlaps UNIX pipes coverage split-alignments BAM support	C++	GPLv2	Linux Mac OS X
Bedutils	NGSUtils is a suite of software tools for working with next-generation sequencing datasets. Staring in 2009, we (Liu Lab @ Indiana University School of Medicine) starting working with next-generation sequencing data. We initially started doing custom coding for each project in a one-off manner. It quickly became apparent that this was an inefficient manner to work, so we started assembling smaller utilities that could be adapted into larger, more complicated, workflows. We have used them for Illumia, SOLiD and 454 sequencing data. We have used them for DNA and RNA resequcing, ChIP-seq, CLIP-Seq, and targeted resequencing (Agilent exome capture and PCR targeting). These tools are also used heavily in our in-house DNA and RNA mapping pipelines. These tools have of great use within our lab group, and so we are happy to make them available to the greater community. NGSUtils is made up of 50+ programs, mainly written in Python. These are separated into modules based on the type of file that is to be analyzed. There are four modules:
Belvu	An X-windows viewer for multiple sequence alignments		Sequence alignment visualisation				Linux
BFAST	Blat-like Fast Accurate Search Tool.	Whole genome resequencing	Read mapping Sequence alignment Genome indexing	parallel execution command line	C	GPL	Solaris UNIX
BFCounter	BFCounter is a program for counting k-mers in DNA sequence data.		K-mer counting		C++	GPLv3
BigBWA	Tool to run the Burrows-Wheeler Aligner-BWA on a Hadoop cluster. It supports the algorithms BWA-MEM, BWA-ALN, and BWA-SW, working with paired and single reads. It implies an important reduction in the computational time when running in a Hadoop cluster, adding scalability and fault-tolerancy.	Whole genome resequencing Genomics Exome capture Sequencing Resequencing Exome and whole genome variant detection Exome analysis Exome	Read mapping Sequence alignment Mapping	Gapped alignment paired-end mapping	Java	GPLv3	Linux 64
BING	biomedical informatics pipeline (BING) for the analysis of NGS data that offers several novel computational approaches to 1. image alignment, 2. signal correlation, compensation, separation, and pixel-based cluster registration, 3. signal measurement and base calling, 4. quality control and accuracy measurement.		Base-calling Sequencing quality control
BioJava	"BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics. "	Genomics			Java	LGPL 2.1
Bionimbus	Cloud environment for analysis of microarray and second generation sequencing data.						Linux Amazon EC2 cloud
BioNumerics	BioNumerics can be used for the analysis of all major applications in bioinformatics	Sequence assembly Whole genome resequencing Genotyping Sequence analysis Comparative genomics Quality control Workflows Data handling Microbial Surveillance Epidemiology	Sequence assembly Read mapping Sequence alignment Annotation Genome visualisation Variant calling Comparative genomics Workflows			Commercial	Windows 7 or Higher
BioPerl	"BioPerl, a community effort to produce Perl code which is useful in biology. "	Genomics			Perl		Cross-Platform
BioPHP	biology tools for php.	Genomics			PHP	GPLv2
Biopieces	The Biopieces are a collection of bioinformatics tools that can be pieced together in a very easy and flexible manner to perform both simple and complex tasks. The Biopieces work on a data stream in such a way that the data stream can be passed through several different Biopieces, each performing one specific task: modifying or adding records to the data stream, creating plots, or uploading data to databases and web services.	Genomics	Sequence alignment Visualisation Sequencing quality control Sequence analysis		Perl Python Ruby C	GPLv2
Biopython	Biopython provides a tool kit for writing bioinformatics and computational molecular biology software in Python.	Sequence analysis Phylogenetics Population genetics Protein structure analysis	Sequence parsing	Various	Python	Biopython License (MIT/BSD style)	Linux Windows Mac OS X
BioRuby	"BioRuby comes with a comprehensive set of free development tools and libraries for bioinformatics and molecular biology, for the Ruby programming language. BioRuby has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports many widely used data formats and provides easy access to databases, external programs and public web services, including BLAST, KEGG, GenBank, MEDLINE and GO."	Genomics			Ruby		Cross-Platform
BioSmalltalk	BioSmalltalk provides an environment to build bioinformatics scripts and applications using the most powerful object technology as of today, the Smalltalk programming environment	Sequence analysis Phylogenetics Population genetics Protein structure analysis	Sequence parsing	Various	Smalltalk		Linux Windows Mac OS X
BiQ Analyzer	BiQ Analyzer is a software tool for easy visualization and quality control of DNA methylation data. With more than 2,000 downloads so far, BiQ Analyzer has become a standard tool for processing DNA methylation data from bisulfite sequencing.	DNA methylation Epigenomics			Java		Windows Linux Mac OS X Solaris
BiQ Analyzer HT	BiQ Analyzer HT is an enhanced version of BiQ Analyzer that provides extensive support for high-throughput bisulfite sequencing. BiQ Analyzer HT facilitates the processing, quality control and initial analysis of single-basepair resolution DNA methylation data. It was developed for deep bisulfite sequencing of one or more loci using the Roche 454 platform, but it easily extends to other sequencing platforms. BiQ Analyzer HT features a biologist-friendly graphical user interface, a fast alignment algorithm and a variety of ways to visualize DNA methylation data.	DNA methylation Sequencing Epigenetics			Java		Windows Linux Mac OS X Solaris
Bis-SNP	BisSNP is a package based on the Genome Analysis Toolkit (GATK) map-reduce framework for genotyping in bisulfite treated massively parallel sequencing (Bisulfite-seq, NOMe-seq and RRBS) on Illumina platform. It uses bayesian inference with either manually specified or automatically estimated methylation probabilities of different cytosine context(not only CpG, CHH, CHG in Bisulfite-seq, but also GCH et.al. in other bisulfite treated sequencing) to determine genotypes and methylation levels simultaneously.	DNA methylation SNP detection Sequencing Genotyping Epigenetics	Bisulfite mapping SNP calling Methylation calling	Accurate SNP and methylation calling in Bisulfite-seq/NOMe-seq/RRBS	Java Perl	MIT	Linux Mac OS X
Bismark	Bismark is a tool to map bisulfite treated sequencing reads and perform methylation calling in a quick and easy-to-use fashion.	Genomics DNA methylation Epigenomics	Read mapping Bisulfite mapping Methylation calling	fast and convenient Bisulfite-Seq output very flexible	Perl	GPLv3	Linux Mac OS X Windows
Bison	Bison allows users with access to a computer cluster to rapidly align whole-genome bisulfite sequencing or RRBS reads. It can align both directional and non-directional libraries and uses bowtie2.	DNA methylation Sequencing Epigenetics	Read mapping Bisulfite mapping Methylation calling	BAM support Bisulfite sequencing MPI	C		Unix-like Linux Mac OS X
BLAST	BLAST finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.		Sequence analysis				Linux
BLAST Ring Image Generator	"BRIG is a cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data. "	Comparative genomics	Visualisation Sequence assembly visualisation				Cross-Platform
BLAT	Fast, accurate spliced alignment of DNA sequences		Read mapping Sequence alignment	Read mapping	C	Freeware	Linux Mac OS X
Blixem	a graphical blast viewer	Sequence analysis Phylogenetics	Sequence alignment visualisation			GPL	Linux
BOAT	Can accurately and efficiently map sequencing reads back to the reference genome.		Read mapping			GPL
Bort	Bort parses Blast output and quantifies hits by contig and read counts.	RNA-Seq quantification			Perl		any
BOW	BOW - Bioinformatics On Windows is essentially a windows port of BWA and SAMTOOLS
Bowtie	Bowtie is an ultrafast, memory-efficient short read aligner.		Read mapping Genome indexing (Burrows-Wheeler)				Mac OS X Linux Windows
BRAT	accurate and efficient tool for mapping short reads obtained from the Illumina Genome Analyzer following sodium bisulfite conversion. Both single and paired ends are supported.	DNA methylation Epigenomics	Bisulfite mapping Mapping			GPLv3
BRCA-diagnostic	Computational screening test for BRCA1/2 mutants in human genomic DNA	Personalised medicine			Perl
BreakDancer	BreakDancer is an application for detecting structural rearrangements and indels in short read sequencing data	Genomics Indel detection Structural variation			Perl C++	GPLv3
Breakpointer	Breakpointer is a fast tool for locating sequence breakpoints from the alignment of single end reads (SE) produced by next generation sequencing (NGS). It adopts a heuristic method in searching for local mapping signatures created by insertion/deletions (indels) or more complex structural variants(SVs). With current NGS single-end sequencing data, the output regions by Breakpoint mainly contain the approximate breakpoints of indels and a limited number of large SVs.	Indel detection Exome and whole genome variant detection	Statistical calculation		C++ Perl	GPL
BreakSeq	Database of known human breakpoint junctions and software to search short reads against them.	Structural variation	Read mapping
BreakTrans	BreakTrans is a computer program that maps predicted gene fusions to genomic structural rearrangements so as to validate both types of events.		Post-analysis
Breakway	Breakway is a suite of programs that take aligned genomic data and report structural variation breakpoints.	Whole genome resequencing Genomics Indel detection Structural variation Genetic variation	SNP calling Sequence analysis	Fast specific UNIX pipes	Perl	GPL	Linux Mac OS X Windows
BS Seeker	Mapping tool for bisulfite treated reads	Epigenomics	Bisulfite mapping		Python
BS-Seq	The source code and data for the "Shotgun Bisulphite Sequencing of the Arabidopsis Genome Reveals DNA methylation Patterning" Nature paper by Cokus et al. (Steve Jacobsen's lab at UCLA). POSIX.	Epigenomics	Bisulfite mapping
BSMAP	short reads mapping software for bisulfite sequencing	DNA methylation	Read mapping Bisulfite mapping	Bisulfite sequencing	C++	GPLv3	Linux 64
BSSim	BSSim: Bisulfite sequencing simulator for next-generation sequencing.	DNA methylation Sequencing Epigenetics	Modelling and simulation	BSSim can allow users to mimic various methylation level.	Python	GPLv3	UNIX Linux Mac OS X Windows
Btrim	Btrim is a fast and lightweight software to trim adapters and low quality regions in reads.		Sequence trimming				Linux
BWA	Fast, accurate, memory-efficient aligner for short and long sequencing reads	Mapping	Read mapping	Gapped alignment paired-end mapping	C	GPLv3 MIT	UNIX
BWA-SW	Fast, accurate, memory-efficient aligner for long sequencing reads	Mapping	Read mapping	Gapped alignment Local alignment	C	GPLv3 MIT	UNIX
CABOG	Celera Assembler is scientific software for DNA research.	Sequence assembly (de novo assembly)	Sequence assembly	Robust to homopolymer run length			Linux
CANGS	CANGS is a flexible and user-friendly utility to trim sequences, filter low quality sequences, and produce input files for further downstream analyses for 454 sequences. CANGS can be used to assign the taxonomic grouping based on similarity with sequences from the NCBI database	Metagenomics Phylogenetics	Sequencing quality control Sequence trimming Primer removal		Perl
CARPET	A web‐based package for the analysis of ChIP‐chip and expression tiling data	ChIP-on-chip	Genotyping		C++
CASHX	Parse, map, quantify and manage large quantities of short-read sequence data.	Transcriptomics	Read mapping
CATCH	A tool for exploring patterns in ChIP profiling data.	ChIP-seq ChIP-on-chip	Sequence alignment Clustering	parallel execution graphical browsing of results	Java	Open Source
CatchAll	Estimate ecological diversity with both parametric and non-parametric estimators.	Metagenomics Population genetics
CEQer	CEQer (Comparative Exome Quantification analyzer) is a graphical, event-driven tool for copy number abnormalities/allelic-imbalance coupled analysis of whole-exome sequencing data. By using case-control matched exome data, CEQer performs a comparative digital exonic quantification to generate CNA data and couples this information with exome-wide LOH and allelic imbalance detection.	Copy number estimation Genetic variation analysis Exome analysis		Copy number and allelic imbalance analyses from matched exomes.	C#	GPLv3	Windows Mac Linux
CexoR	Strand specific peak-pair calling in ChIP-exo data	ChIP-exo	Peak calling	R/Bioconductor package can run on major computer platforms	R	GPL-2 + file LICENSE	Linux Mac OS X Windows
CGA Tools	Tools for viewing, manipulating and converting data from Complete Genomics		File reformatting		C++	Apache License 2.0	Linux UNIX Mac OS X
CHiCAGO	CHiCAGO (Capture HiC Analysis of Genomic Organization) is a set of tools for calling significant interactions in Capture HiC data, such as Promoter Capture HiC.	Epigenomics	Peak calling		R Python	Artistic-2.0	Linux OSX
ChimeraScan	Identifies chimaeric transcripts in RNA-Seq data	Gene structure
ChIP-Seq (application)	The ChIP-seq web server provides access to a set of useful tools performing common ChIP-seq data analysis tasks, including positional correlation analysis, peak detection, and genome partitioning into signal-rich and signal-poor regions. It is an open system designed to allow interoperability with other resources, in particular the motif discovery programs from the Signal Search Analysis (SSA) server.	ChIP-seq	Read mapping Peak calling		C Perl	GPL	Linux Mac OS X
ChIPmeta	Combining data from ChIP-seq and ChIP-chip.	ChIP-seq ChIP-on-chip Transcription factors and regulatory sites	Peak calling
ChIPMunk	ChIPMunk is a fast heuristic DNA motif digger based a on greedy approach accompanied by bootstrapping. ChIPMunk identifies the strong motif with the maximum Kullback Discrete Information Content in a given set of DNA sequences.	ChIP-seq Sequence motifs	Sequence motif comparison Sequence motif discovery	efficient motif discovery for huge datasets up to tens of thousands of sequences; multi-core CPU support; usage of the ChIP-seq base coverage peak data	Java	Freeware	platform-independent
CHiPSeq	From Science Johnson, 2007	ChIP-seq	Peak calling
ChIPseqR	ChIP-seq qanalysis tool	ChIP-seq			R
Chipster	User-friendly NGS data analysis software with built-in genome browser and workflow functionality. Chipster includes tools for ChIP-seq, RNA-seq, miRNA-seq and MeDIP-seq analysis, and functionality for exome-seq and CGH-seq will soon be added.	DNA methylation ChIP-seq RNA-Seq Immunoprecipitation experiment	Read mapping Peak calling Sequence motif recognition Genome visualisation Sequencing quality control Differential expression analysis Sequence trimming Pathway or network analysis Methylation analysis		Java R	GPLv3	platform-independent
ChromaSig	An unsupervised learning method, which finds, in an unbiased fashion, commonly occurring chromatin signatures in both tiling microarray and sequencing data.	ChIP-on-chip Chromatin	Sequence motif recognition		Perl C
ChromHMM	ChromHMM is software for learning and characterizing chromatin states.	Epigenomics	Statistical calculation		Java	GPLv3
Circos	Circos is tool for visualizing data in a circular format. It was developed for genomic data but can work for many other kinds of data as well.	Comparative genomics	Visualisation		Perl		Windows Linux
CisGenome	An integrated tool for tiling array, ChIP-seq, genome and cis-regulatory element analysis	ChIP-seq ChIP-on-chip Sequence motifs	Sequence motif recognition Gibbs sampling Integrated solution Data retrieval		C C++		UNIX Windows
Cistrome	Galaxy-based web service for analysis of ChIP data	ChIP-seq ChIP-on-chip			Python
CLCbio Genomics Workbench	De novo and reference assembly SNP and small indel detection and annotation.	Sequence assembly (de novo assembly) Whole genome resequencing Genomics Transcriptomics ChIP-seq SNP detection Indel detection RNA-Seq Regulatory RNA Mapping	Sequence assembly Sequence assembly (de-novo assembly) Read mapping Sequence alignment Ab-initio gene prediction Adapter removal Annotation Bisulfite mapping SNP calling Heat map generation Sequence assembly validation	Advanced and user-friendly analyses of genomic transcriptomic and epigenomic NGS data in a graphical user-interface. Wizard driven tools and a freely available developer toolkit SIMD implementation multi-threading hybrid assembly Integrated solution	Java C++	Commercial	Windows Mac OS X Linux
Clean reads	clean_reads cleans NGS (Sanger, 454, Illumina and solid) reads.		Sequencing quality control Sequence trimming		Python
CleaveLand	A pipeline for using degradome data to find cleaved small RNA targets.	Regulatory RNA			Perl R	Freeware
CLEVER	CLEVER is a tool to discover structural variations such as (larger) insertions and deletions in genomes from paired-end sequencing reads.	Genomics Structural variation Copy number estimation		command line	C++ Python	GPLv3	any
ClipCrop	a new method and implementation named ClipCrop for detecting SVs with single-base resolution	Whole-genome sequencing
CloudAligner	Hadoop-based short read aligner		Read mapping Hadoop		Java	GPL	cloud
CloudBurst	CloudBurst is a parallel read-mapping algorithm optimized for mapping next-generation sequence data to the human genome and other reference genomes.	SNP detection Genotyping Personalised medicine	Read mapping	parallel execution Hadoop Academic Cloud Computing Initiative	Java
ClustDB	A powerful tool for exact sequence matching						Linux
Cluster Flow	A command-line pipeline tool which uses common cluster managers to run bioinformatics analysis pipelines.		Analysis pipeline		Perl	GPLv3	Linux
CNANorm	A normalization method for Copy Number Aberration in cancer samples.	Genomics Copy number estimation Cancer biology	Peak calling Standardisation and normalisation		R Perl	GPLv2	Linux Mac OS X Windows
CNAseg	We present a novel approach, called CNAseg, to identify CNAs from second-generation sequencing data. It uses depth of coverage to estimate copy number states and flowcell-to-flowcell variability in cancer and normal samples to control the false positive rate.	Structural variation			R
CNB MetaGenomics tools	A number of tools and meta-tools developed at CNB/CSIC for the analysis of metagenomics data (some rely on QIIME).	Metagenomics Sequencing			Bash Perl Python C	EU-GPL	Linux Unix-like POSIX
CnD	Program to detect copy number variation in inbred mouse strains	Copy number estimation			D	GPL
CNVer	CNVer is a method for CNV detection that supplements the depth-of-coverage with paired-end mapping information, where matepairs mapping discordantly to the reference serve to indicate the presence of variation. CNVer combines this information within a unified computational framework called the donor graph, allowing it to better mitigate the sequencing biases that cause uneven local coverage. CNVer can also reconstruct the absolute copy counts of segments of the donor genome, and work with low coverage datasets.	Structural variation Copy number estimation			Perl C++
CnvHMM	WashU copy number variant (CNV) detection algorithm for Illumina/Solexa data.	Structural variation					Linux
CNVkit	CNVkit is a software toolkit to infer and visualize copy number from targeted DNA sequencing data.	Structural variation Copy number estimation	Variant calling	Copy number analysis data visualization	Python	BSD	GNU/Linux Mac OS X
CNVnator	CNV discovery and genotyping from read-depth analysis of personal genome sequencing	Genotyping Copy number estimation
CNVseq	CNV-seq, a method to detect copy number variation using high-throughput sequencing. pubmed	Copy number estimation			Perl R
CompreheNGSive	compreheNGSive is an interactive visualization of the end results of the next-generation sequencing pipeline.	Next Generation Sequencing	Visualisation		Python Qt	LGPL	Mac OS X Linux
CoNAn-SNV	CoNAn-SNV is a probabilistic framework for the discovery of single nucleotide variants in WGSS data. This software explicitly integrates information about copy number state of different genomic segments into the inference of single nucleotide variants.	SNP detection			C
ConDeTri	ConDeTri is a content dependent read trimming software for Illumina/Solexa sequencing data	Genomics RNA-Seq Sequencing	Sequence trimming		Perl
ContEst	GATK tool to estimate amount of cross-individual contaminating sequence in a dataset	Metagenomic sequencing	Sequencing quality control		Java	BSD
Contra	Copy number analysis for exome-sequencing / targeted-resequencing. Two methods of analysis available: Case vs Control, or Case vs Baseline. Function available for creating a baseline from multiple samples.	Genomics Sequencing Copy number estimation Cancer biology		Copy number analysis baseline (pseudo-control) creation	Python R	GPLv3	Linux 64 Linux
Contrail	A Hadoop based genome assembler for assembling large genomes in the clouds	Sequence assembly (de novo assembly)	Sequence assembly Sequence assembly (de-novo assembly) Hadoop
CopySeq	CopySeq analyzes the depth-of-coverage of whole genome resequencing data to predict CNVs and to infer quantitative locus copy-number genotypes.	Structural variation Genotyping Personalised medicine Copy number estimation			Java R		Mac OS X Linux
Coral	Corrects sequencing errors in short read data via multiple alignments		Sequence error correction		C++
CORAL (Contig Ordering Algorithm)	An algorithm has been developed to order fingerprinted clones within contigs.		Sequence error correction		Java
Cortex	Cortex is an efficient and low-memory software framework for analysis of genomes using sequence data. Cortex allows de novo assembly of variants without having to do a consensus assembly first. Also allows comparison of genomes without using consensus, and alignment of sequence data to a de Bruijn graph	Genomics	Sequence assembly Variant calling		C	GPLv3
CPTRA	Integrated transcriptome analysis from Sanger, 454, Solexa, SOLiD, etc reads	RNA-Seq alignment RNA-Seq quantification			Python
CRAC	CRAC is a mapping software specialized for RNA-Seq data. It detects mutations, indels, splice or fusion junctions in each single read.	RNA-Seq alignment SNP detection Indel detection RNA-Seq quantification Alternative splicing Gene structure	Read mapping Genome indexing (Burrows-Wheeler)		C++	CeCILL	Linux Linux 64 Mac OS X
CRAVAT	CRAVAT is a web-based resource for cancer-related analysis of genomic variants (single base substitutions and indels). CRAVAT provides scoring, sorting, filtering, and interactive visualizations to assist with identification of important variants.	Genomics Genetic variation Genetics	Annotation Variant prioritisation SNP annotation Variant classification Sequence annotation	Gene-based annotation Detailed Reports Easy-to-use point-and-click web interface GUI HTML5 canvas graphics Identify effects of SNPs on transcripts Interactive Multiple replicates information used; automated pipeline; easy genomic annotation; finding hotspots; SNP annotation User-friendly User Management Variant annotation and analysis			Web Linux
CRISP	Identifies rare and common variants in pooled sequencing data	SNP detection			Python
Crossbow	Crossbow is a cloud-computing software tool that combines the aligner BOWTIE and the SNP caller SOAPsnp.	SNP detection	Read mapping
CUDA-EC	A scalable parallel algorithm for correcting sequencing errors in high-throughput short-read data so that error-free reads can be available before DNA fragment assembly.		Sequencing quality control	read error correction	C
Cufflinks	Cufflinks assembles transcripts and estimates their abundances in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one.	Transcriptomics RNA-Seq alignment RNA-Seq RNA-Seq quantification Alternative splicing	Read mapping Transcriptome assembly Differential expression analysis			Boost
CummeRbund	Allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations.	RNA-Seq quantification	Visualisation
Curtain	Curtain is a Java wrapper around next-generation assemblers such as Velvet which allows the incremental introduction of read-pair information into the assembly process. This enables the assembly of larger genomes than would otherwise be possible within existing memory constraints.	Sequence assembly (de novo assembly)	Sequence assembly Sequence assembly (de-novo assembly)			Apache License 2.0
Cutadapt	remove adapter sequences from high-throughput sequencing data using alignment				Python Cython	MIT
DCLIP	dCLIP is a Perl program for discovering differential binding regions in two comparative CLIP-Seq (HITS-CLIP, PAR-CLIP or iCLIP) experiments.	CLIP-Seq HITS-CLIP PAR-CLIP ICLIP	Sequence alignment analysis		Perl C		UNIX Unix-like
DecGPU	Parallel and distributed error correction algorithm for high-throughput short reads.	Sequence assembly (de novo assembly)	Sequence error correction		C++	GPLv3	Linux
DeconSeq	DeconSeq can be used to automatically detect and efficiently remove any type of sequence contamination from metagenomic datasets, including human or other host sequences. The tool uses a modified version of the BWA-SW aligner and can be applied to longer-read datasets (150+bp read length). DeconSeq is available as both standalone and web-based versions.	Genomics Transcriptomics Metagenomics	Sequence contamination filtering		Perl C	GPLv3	UNIX Mac OS X
DeepTools	User-friendly tools for the normalization and visualization of deep-sequencing data.	Genomics ChIP-seq	Visualisation Conversion Standardisation and normalisation	Data Visualisation coverage analysis File reformatting normalization GC plot analysis	Python	GPLv3	Linux Mac OS X
DeFuse	deFuse is a software package for gene fusion discovery using RNA-Seq data. The software uses clusters of discordant paired end alignments to inform a split read alignment analysis for finding fusion boundaries. The software also employs a number of heuristic filters in an attempt to reduce the number of false positives and produces a fully annotated output for each predicted fusion	RNA-Seq Gene structure
DEGseq	an R package to identify differentially expressed genes or isoforms for RNA-seq data from different samples	RNA-Seq quantification	Differentially expressed gene identification		R
DESeq	DESeq is an R package to analyse count data from high-throughput sequencing assays such as RNA-Seq and test for differential expression. The latest version is DESeq2 (released April 2013).	ChIP-seq RNA-Seq quantification	Sequencing quality control Statistical testing		R	GPLv3	UNIX Windows Mac OS X
DIAL	A computational pipeline for identifying single-base substitutions between two closely related genomes without the help of a reference genome.	SNP detection Comparative genomics			C Python	MIT	Linux
DiBayes	Bayesian identification of SNPs in color space (SOLiD) data	SNP detection				GPL
DiffBind	Differential Binding Analysis of ChIP-seq peak data Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.	ChIP-seq	Differential binding sites	Multiple replicates information used; automated pipeline; finding hotspots;	R	Artistic-2.0	Linux Mac OS X Windows
Diffreps	diffReps is developed to find different peaks in ChIP-seq. It scans the whole genome using a sliding window, performing millions of statistical tests and report the significant hits. diffReps takes into account the biological variations within a group of samples and uses that information to enhance the statistical power. Considering biological variation is of high importance, especiallly for in vivo brain tissues.	ChIP-seq	Differential Binding	Multiple replicates information used; automated pipeline; easy genomic annotation; finding hotspots;	Perl	GPLv3	Linux Windows Mac OS X
Dindel	Calls small indels from short-read sequence data	Indel detection	Localised reassembly
DiscoSnp	discoSnps : qualitative de-novo SNP caller. Extremely low memory and time efficient. No reference genome needed. Call both homozygous and heterozygous SNPs.	Sequence assembly (de novo assembly) Sequencing Genotyping Comparative genomics High-throughput sequencing Population Genomics	Sequence assembly (de-novo assembly) Read depth analysis	de novo (reference free) SNP calling	C++	CeCILL	Unix-like iOS
DNA Baser	Tool for manual and automatic sequence assembly, analysis, editing, sample processing, metadata integration, file format conversion and mutation detection.	SNP detection Structural variation	Sequence assembly Sequence analysis Sequence assembly editing	Portable. Does not require installation. Can run from USB stick. Only 3MB.		Commercial Freeware	Windows
DNA Chromatogram Explorer	DNA Chromatogram Explorer is a Windows Explorer clone dedicated to DNA sequence analysis and manipulation.	Sequence analysis	File reformatting Chromatogram visualisation	Portable. Does not require installation. Can run from USB stick. Only 1MB.		Freeware	Windows
DNAA	DNAA (DNA Analysis) software for analysis of Next-Generation Sequencing data.	DNA methylation SNP detection Structural variation	Sequencing quality control Modelling and simulation Statistical calculation			GPL
DNaseR	DNase I footprinting analysis of DNase-seq data in R	DNase-seq	Peak calling Nucleic acid sequence feature detection	R/Bioconductor package can run on major computer platforms	R	GPL-2 + file LICENSE	Linux Mac OS X Windows
DNAzip	A series of techniques that in combination reduces a single genome to a size small enough to be sent as an email attachment.		File reformatting		C++
DrFAST	Fast mapper for dibase encoded data.
DSAP	Automated multiple-task web service designed to provide a total solution to analyzing deep-sequencing small RNA datasets generated by next-generation sequencing technology	Transcriptomics Regulatory RNA					browser based
DSGseq	This program aims to identify differentially spliced genes from two groups of RNA-seq samples.	RNA-Seq Alternative splicing Gene expression	Statistical calculation Differential expression analysis RNA-Seq analysis		C R	Commercial Freeware	Linux Windows Mac OS X
DSRC	Compression algorithm for genomic data in FASTQ format		File reformatting
E-miR	Perl tools for processing miRNA sequencing data	Transcriptomics Regulatory RNA
Ea-utils	FASTQ processing utilities		Sequencing quality control Sequence trimming		C++	MIT
EagleView	EagleView is an information-rich genome assembler viewer with data integration capability.		Sequence assembly visualisation
EagleView genome viewer	EagleView is an information-rich genome assembler viewer with data integration capability.		Visualisation				Linux Windows Mac OS X
EaSeq	EaSeq is developed for user-friendly exploration, visualization and analysis of genome-wide single-read sequencing data (mainly ChIP-seq). Both individual genomic loci and populations of loci can be visualized e.g. as plots of average signals, scatter diagrams, or clustered heatmaps. The underlying loci can then be inspected just by selecting them in the plots - or they can be 'gated out' for further analysis. EaSeq also integrates more than 20 tools for analysis, including peak-finding, quantitation, normalization, clustering, distance analysis, randomization, scoring, and normalization. Finally, it automatically generates legends and descriptions of the handling and can store plots together with underlying data and these descriptions as a single compact session file.	ChIP-Seq	Visualisation Peak calling Viewer Clustering Integrated solution Genome visualisation Analysis Biological interpretation Regression analysis Correlation Filtering Genomic region matching Format conversion Read summarisation Enrichment Global test Visualisation Quality assessement And more...	Interactive User-friendly GUI WYSIWYG ChIPseq analysis Data Visualisation Data analysis Genome Viewer Integrated solution Memory efficient Multicore Integrated tutorials Automatic documentation Integrated chat forum		Freeware Custom Licence	Windows 7 or Higher
Easyfig	Genome comparison figure generator	Comparative genomics	Comparative genomics		Python	GPLv3	Windows Mac OS X GNU/Linux
EBCall	EBCall is a software package for somatic mutation detection (including InDels). EBCall uses not only paired tumor/normal sequence data of a target sample, but also multiple non-paired normal reference samples for evaluating distribution of sequencing errors, which leads to an accurate mutaiton detection even in case of low sequencing depths and low allele frequencies.
ECHO	Reference-free short read error correction from diploid genomes, with explicit modeling of heterozygous sites.	SNP detection Indel detection	Sequence error correction		Python C++	BSD
EDENA	An assembler dedicated to process the millions of very short reads produced by the Illumina Genome Analyzer.		Sequence assembly
EdgeR	edgeR is an R/Bioconductor software package for statistical analysis of replicated count data. Methods are designed for assessing differential expression in comparative RNA-Seq experiments, but are generally applicable to count data from other genome-scale platforms (ChIP-seq, MeDIP-Seq, Tag-Seq, SAGE-Seq etc).	DNA methylation ChIP-seq RNA-Seq RNA-Seq quantification Gene expression analysis	Statistical calculation		R	LGPL	Windows Mac OS X UNIX
ELAND	Efficient Large-Scale Alignment of Nucleotide Databases. Whole genome alignments to a reference genome. Written by Illumina author Anthony J. Cox for the Solexa 1G machine.		Sequence alignment			Commercial
EMBF	Frequency-based, de novo short-read clustering method that organizes erroneous short sequences originating in a single abundant sequence into a tree structure; in this structure, each “child” sequence is considered to be stochastically derived from its more abundant “parent” sequence with one mutation through sequencing errors.		Mapping
Epigenome	A bioinformatic pipeline that scores epigenetic alterations according to strength and significance and links them to potentially affected genes.	Epigenomics	Bisulfite mapping		R Python
EpiGRAPH	EpiGRAPH enables biologists to analyze genome and epigenome datasets with powerful statistical and machine learning methods. In a typical workflow, the user uploads a set of genomic regions of interest (e.g. experimentally mapped enhancers, hotspots of epigenetic regulation or sites exhibiting disease-specific alterations), and EpiGRAPH searches a large database of (epi-) genomic attributes for significant overlap and correlation with the regions in the input dataset. Furthermore, EpiGRAPH can predict the status of genomic regions that were not included in the input dataset.	Epigenomics Machine learning	Statistical calculation				browser based
ERANGE	ERANGE is a Python package for doing RNA-seq and ChIP-seq.	ChIP-seq RNA-Seq alignment RNA-Seq quantification DNA transcription		RNAseq analysis Chipseq analysis	Python
ERDS	ERDS is a free, open-source software, designed for detection of copy number variants (CNVs) on human genomes from next generation sequence data. It uses paired Hidden Markov models (PHMM) based on the expected distribution of read depth of short reads and the presence of heterozygous sites. ERDS is NOT good for whole exome data.	Copy number estimation
ERGO Genome Analysis and Discovery System	ERGO provides a systems-biology informatics toolkit centered on comparative genomics to capture, query and visualize sequenced genomes. Building upon the most comprehensive genomic database available anywhere integrated with the largest collection of microbial metabolic and non-metabolic pathways and using Igenbio's proprietary algorithms, ERGO assigns functions to genes, integrates genes into pathways, and identifies previously unknown or mischaracterized genes, cryptic pathways and gene products.	Transcriptomics Metagenomics Transcription factors and regulatory sites Phylogenetics Comparative genomics SNP Functional genomics Gene structure Exome analysis Genome Wide Association Studies Metabolic pathways	Sequence alignment SNP detection SNP annotation Gene expression analysis Pathway or network analysis Sequence annotation Sequence functional annotation Metabolic network modelling			Commercial	Web
ERNE	Extended Randomized Numerical alignEr for accurate alignment of NGS reads. It can map bisulfite-treated reads.	Sequence alignment Genomics DNA methylation Sequencing Epigenetics	Read mapping Bisulfite mapping	Bisulfite sequencing sequence alignment	C++	GPLv3	Linux Mac OS X Windows
Error Correction Evaluation Toolkit	Evaluation of error correction results	Data handling	Sequencing quality control		Python Perl		POSIX
Est2assembly	Processes raw sequence data from Sanger or 454 sequencing into a hybrid de-novo assembly, annotates it and produces GMOD compatible output, including a SeqFeature database suitable for GBrowse.	Genomics RNA-Seq alignment	Sequence assembly
ESTcalc	Estimation of project costs for RNA-Seq study.	RNA-Seq			Perl
EULER	EULER-SR is a program for de novo assembly of reads. Contrary to the overlap-layout approach, EULER-SR uses a de Bruijn graph to construct an assembly. The assembly of a genome corresponds to an Eulerian path in the de Bruijn graph. Long (possibly erroneous) reads, and mate-pairs are used to determine parts of the correct Eulerian traversal in the assembly.		Sequence assembly Sequence assembly (de-novo assembly)		C++ Perl		Linux
ExomeCNV	Identifies copy number variation from targeted exome sequencing data	Exome capture Copy number estimation			R
ExomeCopy	CNV detection from exome sequencing read depth	Copy number estimation Exome and whole genome variant detection Exome analysis		simultaneous normalization and segmentation	R	GPL 2.0+	Linux Windows Mac OS X
ExomePicks	ExomePicks is a program that suggests individuals to be sequenced in a large pedigree.
Exonerate	Various forms of alignment (including Smith-Waterman-Gotoh) of DNA/protein against a reference. Authors are Guy St C Slater and Ewan Birney from EMBL. C for POSIX.		Sequence alignment		C	GPL	Linux
FAAST	Flowspace Assisted Alignment Search Tool		Read mapping				Linux
FaBox	Tools for splitting, joining and otherwise manipulating FASTA format sequence files.	Sequence assembly Phylogenetics
FACS	Rapid and accurate classification of sequences as belonging or not belonging to a reference sequence.	Metagenomics			Perl f	GPLv2	Linux
Falcon	FALCON: experimental PacBio diploid assembler	Sequence assembly	Sequence assembly
FAST: Fast Analysis of Sequences Toolbox	The FAST Analysis of Sequences Toolbox (FAST) is a set of Unix tools (for example fasgrep, fascut, fashead and fastr) for sequence bioinformatics modeled after the Unix textutils (such as grep, cut, head, tr, etc).	Genomics Sequence analysis	Sequence analysis Sequence parsing				GNU/Linux Mac OS X
FastQ Screen	FastQ Screen provides a simple way to screen a library of short reads against a set of reference libraries. Its most common use is as part of a QC pipeline to confirm that a library comes from the expected source, and to help identify any sources of contamination.	Genomics Transcriptomics	Read mapping Sequencing quality control	Summarises the mapping of a library against a series of reference sequences	Perl	GPLv3	Linux Mac OS X Windows
FastQC	FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines.		Sequencing quality control		Java	GPLv3	UNIX Windows
FastQValidator	Checking that FastQ files are follows standards	Quality control	Sequencing quality control		C++
FDM	Detects differential transcription in RNA-Seq data	RNA-Seq quantification
FeatureCounts	featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package.	Next Generation Sequencing	Read summarisation	read summarisation	R C	GPLv3	Linux 64 Mac OS X Mac OS X; x86 64
FHiTINGS	"FHiTINGS is designed for use in rapidly identifying, classifying, and parsing internal transcribed spacer (ITS) DNA sequences after a BLASTn search. This software is useful for fungal ecology studies using next generation sequencing (NGS)."	Metagenomics Comparative genomics	Sequence alignment		Python		Cross-Platform
Figaro	Figaro is a software tool for identifying and removing the vector from raw DNA sequence data without prior knowledge of the vector sequence.	Sequencing	K-mer counting	AMOS	C++ Perl	Artistic License	UNIX
Filter	Produces a filtered version of an sRNA dataset, controlled by several user-defined criteria, including sequence length, abundance, complexity, transfer and ribosomal RNA removal.	Workflows	Sequence contamination filtering	multi-threading	Java	Custom Licence	Linux 64 Windows Mac OS X
FindPeaks 3.1	Findpeaks was developed to perform analysis of ChIP-seq experiments.	ChIP-seq	Peak calling			GPLv3
FindPeaks 4.0 (Vancouver Short Read Package)	The Vancouver Short Read Analysis Package (VSRAP) contains the FindPeaks application for Chip-Seq and RNA-Seq analysis, as well as utilities for SNP finding, working with aligned sequence files and a nascent database for storing SNPs across multiple libraries.	Genomics SNP detection	Peak calling Formatting Sequence alignment analysis	command line	Java	GPL	Linux Windows Mac OS X
FLASH	Identifies paired-end reads which overlap in the middle, converting them to single long reads		Sequence assembly Read pre-processing	combining forward and reverse reads	C	Open Source	Linux 64
Flexbar	Flexible barcode and adapter processing for next-generation sequencing platforms	Genomics	Adapter removal Sequence trimming DNA barcoding Quality control Read pre-processing	Paired read support separate barcode reads multi-threading	C++	GPLv3	Linux Windows Mac OS X
Flower	Tool for reformatting SFF files into other formats or tab-delimited				Haskell
FlowSim	Tool for simulating errors in 454 sequencing data		Sequence error correction Modelling and simulation		Haskell
Flux	FluxCapacitor s a computer program to predict splice form abundancies from reads of an RNA-seq experiment. FluxSimulator can generate simulated data for testing RNA-seq pipelines	RNA-Seq	Modelling and simulation
Forge	De novo assembly using a combination of next-generation and Sanger reads	Sequence assembly (de novo assembly) Genomics	Sequence assembly
FragGeneScan	Application for finding (fragmented) genes in short reads	Genomics Metagenomics			C Perl	GPL
FrameDP	Sensitive peptide detection on noisy matured sequences. A self-training integrative pipeline for predicting CDS in transcripts which can adapt itself to different levels of sequence qualities.	RNA-Seq
FreClu	a frequency-based, de novo short-read clustering method that organizes erroneous short sequences originating in a single abundant sequence into a tree structure; in this structure, each “child” sequence is considered to be stochastically derived from its more abundant “parent” sequence with one mutation through sequencing errors. The root node is the most frequently observed sequence that represents all erroneous reads in the entire tree, allowing the alignment of the reliable representative read to the genome without the risk of mapping erroneous reads to false-positive positions.	RNA-Seq alignment	Read mapping
Freebayes	Bayesian genetic variant detector (SNPs, indels, MNPs)	Genomics				MIT
FREEC	A tool for control-free copy number alteration (CNA) detection using deep-sequencing data, particularly useful for cancer studies.	Copy number estimation					Linux Linux 64 Windows
FusionAnalyser	FusionAnalyser is a new graphical, event-driven tool dedicated to the identification of driver fusion rearrangements in human cancer through the analysis of paired-end high-throughput transcriptome sequencing data. Tested on Illumina. Requires short, paired-end sequences.	Gene structure High-throughput sequencing		Advanced and user-friendly analysis of RNA-seq data for fusion discovery	C#	GPLv3	Windows Linux
FusionCatcher	FusionCatcher searches for novel/known somatic fusion genes, translocations, and chimeras in RNA-seq data (paired-end or single-end reads from Illumina NGS platforms like Solexa/HiSeq/NextSeq/MiSeq) from diseased samples).	RNA-Seq Gene structure	Sequence alignment		Python	GPLv3	NIX
FusionHunter	Identifies gene fusions in RNA-Seq data	RNA-Seq			Perl C		Linux Linux 64
FusionMap	Detects fusion events in both single- and paired-end datasets from either RNA-Seq or gDNA-Seq studies and characterize fusion junctions at base-pair resolution.	Gene structure	Split-read mapping		C#	Commercial Freeware	Windows Linux Linux 64
FusionSeq	Identifies fusion transcripts from paired end RNA-Seq data.	RNA-Seq Gene structure	Sequence alignment analysis		C	Creative Commons - Attribution; Non-commercial 2.5	Mac OS X UNIX Linux
Fuzzypath	Assembler	Genomics	Sequence assembly Sequence assembly (de-novo assembly)
G-Mo.R-Seq	G-Mo.R-Se is a method aimed at using RNA-Seq short reads to build de novo gene models.	RNA-Seq alignment				CeCILL	Linux
G-SQZ	Huffman coding-based sequencing-reads specific representation scheme that compresses data without altering the relative order.		File reformatting		C++
Galaxy	"Galaxy is an open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses. "	Sequence assembly Whole genome resequencing Genomics Comparative genomics Functional genomics	Sequence assembly Sequence alignment Visualisation Sequencing quality control		Python		Cross-Platform
Galign	Identifies polymorphisms between sequence reads obtained using Illumina/Solexa technology and a reference genome	SNP detection	Read mapping			GPL
Gambit	A cross-platform GUI for sequence visualization and analysis.		Visualisation			GPL 2.0+ Commercial
GAMES	GAMES (Genomic Analysis of Mutations Extracted by Sequencing) is a tool for mining and prediction of functional effect of mutation.	SNP	SNP detection Indel detection SNP annotation		Perl		Linux
GASSST	Fast and accurate aligner for short an long reads		Sequence alignment Mapping	Gapped alignment short and long reads	C++	CeCILL	Linux
GASV	Software for classification and comparison of structural variants measured via paired-end sequencing and/or array-CGH.	Structural variation				GPLv3
GATK	The Genome Analysis Toolkit (GATK) is a structured programming framework designed to enable rapid development of efficient and robust analysis tools for next-generation DNA sequencers. The GATK solves the data management challenge by separating data access patterns from analysis algorithms, using the functional programming philosophy of Map/Reduce	SNP detection	Localised reassembly Statistical calculation		Java Python
GBrowse	Genome Viewer		Visualisation	Genome Viewer	Perl	Open Source	Linux Mac OS X Windows
GeeFu	Database tool for genomic assembly and feature data	Genomics	Sequence assembly		Ruby
GEM	GEM is a java software tool to analyze transcription factor binding ChIP-seq/ChIP-exo data. It predicts binding events, performs de novo motif discovery and use the motif to improve the binding event calling. It calls binding events right at (or very close to ) the motif positions, deconvolves closely spaced homotypic binding events and accurately discovers binding motifs.	ChIP-seq	Peak calling Sequence motif discovery	probabilistic mixture model motif prior multi-threading	Java	Commercial Freeware	Cross-Platform
GEM library	A set of very optimized tools for indexing/querying huge genomes/files. Provided so far: a very fast exact mapper, and an unconstrained split-mapper		Read mapping		C Python OCaml	GPLv3
GENALICE MAP	From FASTQ to VCF in 30 min or less. Ultra-fast Next-Generation Sequencing (NGS) read alignment and variant calling solution.	Genomics	Read mapping Variant calling	ultrafast alignment and variant calling		Commercial	Linux
GENE-Counter	GENE-counter is a computational pipeline for analyzing RNA-Sequencing (RNA-Seq) data for differential gene expression	RNA-Seq					Linux Mac OS X
Genedata Expressionist	Genedata Expressionist performs efficient and quality compliant analysis of next generation sequencing (NGS) and other genomic profiling data	Genomics Transcriptomics DNA methylation ChIP-seq SNP detection Indel detection RNA-Seq Sequencing Laboratory information management Copy number estimation Epigenetics Gene structure	Read mapping Sequence alignment Annotation Bisulfite mapping Clustering Genome visualisation Sequencing quality control Sequence analysis Statistical calculation Gene expression analysis RNA-Seq analysis	Data processing Data management Data analysis Data storage Downstream analysis Pipeline Management Workflows Reporting Audit Trail User Management Data Visualisation	Java	Commercial	Windows Linux
Geneious	Search, organize and analyze genomic and protein information of any size via desktop program that provides publication ready images to enhance the impact of your research.	Sequence assembly (de novo assembly) Genomics RNA-Seq Metagenomics Epigenomics Structural variation Sequence analysis Phylogenetics Population genetics	Sequence assembly Read mapping Sequence alignment Visualisation Annotation Sequence assembly validation Genome visualisation Variant calling DNA barcoding Sequence motif discovery		Java	Commercial	Windows Mac OS X Linux Solaris
GeneProf	GeneProf is a web-based, graphical software suite and database resource for high-throughput-sequencing experiments (RNA-seq and ChIP-seq).	ChIP-seq RNA-Seq	Read mapping Visualisation Peak calling Sequencing quality control Differential expression analysis	User-friendly wizards tutorials examples very flexible reproducible transparent extensible API	Java JavaScript	Commercial Freeware	browser based
GeneTalk	GeneTalk, a web-based platform, that can filter, reduce and prioritize human sequence variants from NGS data and assist in the interpretation of personal variants in clinical context.	Structural variation	Annotation Sequence contamination filtering Sequence analysis Variant calling Genetic variation analysis Plotting and rendering Exome analysis Variant classification	Easy-to-use point-and-click web interface data visualization data filtering Fast SNP annotation SNP calling Variant annotation and analysis variant counting	Ruby JavaScript	Freemium
Genomatix Mining Station (GMS)	The Genomatix Mining Station (GMS) offers mapping of NGS reads onto genomes, transcriptomes and splice-junction libraries. It is a client-server based solution and can be controlled through an intuitive GUI or via command-line. It covers different tasks such as, as genomic positioning, SNP detection, splice analyses and genomic enrichments.	ChIP-seq SNP detection RNA-Seq	Sequence assembly Read mapping SNP calling Correlation	Client-server based system allows for command-line and web-based access. Grid engine is used for job scheduling and mapping is run on multiple cores. Can be combined with a Genomatix Genome Analyzer (GGA) for a fully integrated NGS solution.	C++ Java Flash	Commercial	Windows Mac OS X Linux
Genome Trax	Genome Trax™ enables you to identify human genome variations of functional significance by mapping your NGS data to known elements such as disease mutations and regulatory sites.	SNP detection Indel detection Structural variation Regulatory genomics				Commercial
GenomeBrowse	A free genome browser for exploring sequencing pile-up and coverage data with numerous annotation tracks hosted on the cloud.	Sequence assembly (de novo assembly) Sequence alignment Whole genome resequencing Genomics Sequencing Sequence analysis Genetics Exome and whole genome variant detection Exome analysis Next Generation Sequencing	Visualisation Sequence assembly visualisation Sequence alignment visualisation				Windows Linux Mac OS X
Genomedata	Genomedata is a format for efficient storage of multiple tracks of numeric data anchored to a genome. The format allows fast random access to hundreds of gigabytes of data, while retaining a small disk space footprint.	Storage	Signal		Python C	GPL	Linux Mac OS X
GenomeJack	GenomeJack is a genome browser specialized in next-generation sequencing data. Advantages are intuitive interface and smooth drag'n drop response.	Genomics Personalised medicine	Visualisation		Java	Freeware	Windows Mac OS X Linux
GenomeMapper	GenomeMapper is a short read mapping tool designed for accurate read alignments. It quickly aligns millions of reads either with ungapped or gapped alignments. It can be used to align against multiple genomes simulanteously or against a single reference.		Read mapping Sequence alignment
Genometa	Genometa is a Java based local bioinformatics program which allows rapid analysis of metagenomic short read datasets. Millions of short reads can be accurately analysed within minutes and visualised in the browser component. A large database of diverse bacteria and archaea has been constructed as a reference sequence.	Genomics Metagenomics	Read mapping Visualisation	Read mapping Data Visualisation	Java		Linux Mac OS X Windows
GenomeTools	The GenomeTools genome analysis system is a free collection of bioinformatics tools for genome informatics.1.3.6	Genomics		Integrated solution	C	BSD	POSIX Linux Mac OS X OpenBSD Windows (Cygwin) UNIX
GenomeView	GenomeView is a next-generation stand-alone genome browser and editor initiated in the BSB group at VIB and currently developed at Broad Institute. It provides interactive visualization of sequences, annotation, multiple alignments, syntenic mappings, short read alignments and more. Many standard file formats are supported and new functionality can be added using a plugin system.	Genomics Transcriptomics Sequencing Sequence analysis Comparative genomics Quality control	Visualisation Data retrieval Genome visualisation Sequence alignment visualisation Plotting and rendering	Visualisation of a multitude of genomics data	Java	GPL	platform-independent
GenomicTools	GenomicTools is a platform for the analysis and manipulation of high-throughput sequencing data such as RNA-seq and ChIP-seq.	Genomics ChIP-seq RNA-Seq	Peak calling Heat map generation Genome comparison	create custom pipelines feature overlaps identify binding site peaks in ChIP-seq data create read profiles create read heatmaps	C C++	GPLv2
GenoMiner	A proprietary NGS analysis solution. Powerful hardware comes with preinstalled software, organized in workflows.	Sequence assembly Sequence assembly (de novo assembly) ChIP-seq RNA-Seq	Sequence assembly Sequence alignment Peak calling Sequence error correction Plotting and rendering Mutation detection Gene expression profiling	GenoMiner provide workflows for Reference assembly De novo assembly ChIPSeq RNASeq and more. You upload your files at the beginning and you get the results at the end while you can choose from various tools to use for analysis.	Java	Commercial	Linux
GenoREAD	GenoREAD is a web-based, sequence verification software that can be used to compare Sanger sequencing trace files against a reference sequence. Users can either submit their sequencing results one clone at a time, or they can submit a series of clones (as a project) to run at once. Results can be viewed online or downloaded.	Sequencing Clone verification	Sequence assembly Read mapping Sequence alignment		Perl PHP JavaScript		Linux 64
GenoViewer	A feature rich NGS assembly viewer/browser.		Viewer	large file loading multicontig handling SNP/InDel/Read Error display and search mutation table generation and export consensus sequence generation and export	Java	Freeware	platform-independent
GensearchNGS	A user friendly framework for re-sequencing in a diagnostics context: searching for mutations/variants, especially on well known genes.	Exome capture	Sequence alignment Sequence alignment visualisation Read alignment Variant prioritisation Mutation detection	Plugin framework Cafe Variome submission	Java	Commercial	UNIX Windows
GenVision	GenVision is a genomic visualization software package that is fully integrated with Lasergene and is designed to support easy generation of publication quality graphics and maps.	Genomics	Visualisation			Commercial	Windows Mac OS X
Geoseq	Instead of mapping the reads to reference genomes or sequences, Geoseq maps a reference sequence against the sequencing data. It is web-based, and holds pre-computed data from public libraries.	Resequencing	Read mapping
GigaBayes	A short-read SNP and short-INDEL discovery program.	Genomics SNP detection	SNP calling
GimmeMotifs	GimmeMotifs is a de novo motif prediction pipeline, especially suited for ChIP-seq datasets. It incorporates several existing motif prediction algorithms in an ensemble method to predict motifs and clusters these motifs using the WIC similarity scoring metric.	ChIP-seq Epigenomics Gene regulation	Sequence motif comparison		Python	MIT	Linux
Girafe	The R/Bioconductor package girafe facilitates the functional exploration of alignments of sequence reads from next-generation sequencing data to a genome. It allows users to investigate the genomic intervals together with the aligned reads and to work with, visualise and export these intervals.		Sequence alignment		R
Gk arrays	Gk-arrays are a data structure to index the k-mers in a collection of reads.	Genomics Transcriptomics Metagenomics	Sequence assembly Read mapping Sequence error correction	programming library	C++	CeCILL-C license	Linux Linux 64 Mac OS X any
GlobalSeq	Testing for association between RNA-Seq and high-dimensional data	RNA-Seq ChIP-Seq MicroRNA-Seq Meth-Seq	Omnibus test Global test Joint significance test		R	GPL-3	cross-platform
GMAP	GMAP (Genomic Mapping and Alignment Program) for mRNA and EST Sequences.		Read mapping Sequence alignment		C Bourne shell		UNIX
Gnumap	The Genomic Next-generation Universal MAPper (gnumap) is a program designed to accurately map sequence data obtained from next-generation sequencing machines (specifically that of Solexa/Illumina) back to a genome of any size. Currently, gnumap is designed to be used with the _int.txt data received from the Solexa/Illumina machine.		Read mapping		C++
Goby framework	Goby is a next-gen data management framework designed to facilitate the implementation of efficient next-gen data analysis pipelines.	RNA-Seq	File reformatting		Java	GPLv2
Golden Helix	Golden Helix is a bioinformatic software provider and analytic service provider.	Genomics SNP detection Epigenomics Sequencing Copy number estimation Data handling	Annotation Genome visualisation Sequencing quality control Sequence contamination filtering Variant calling Statistical calculation Collapsing methods Variant classification				Windows Linux Mac OS X
Goseq	An R package to detect Gene Ontology (GO) categories and other categories of genes (such as KEGG pathways) that are over/under represented in an RNA-seq data.	RNA-Seq quantification	Gene set testing		R	LGPL	UNIX Windows
Gowinda	Gowinda: unbiased analysis of gene set enrichment for Genome Wide Association Studies	Genomics Sequencing Population genetics Population Genomics	Ontology comparison Functional enrichment Genome-wide association study	Multicore	Java	Mozilla Public License	Mac OS X Linux Windows
GPS	GPS is a high spatial resolution peak detection algorithm for ChIP-seq data.	Genomics ChIP-seq Epigenomics Transcription factors and regulatory sites	Peak calling	multi-threading	Java	Commercial Freeware	Cross-Platform
GPSeq	Analyze RNA-seq data to estimate gene and exon expression, identify differentially expressed genes, and differentially spliced exons	RNA-Seq quantification			R C
GRIDSS	GRIDSS is a structural variant caller which combines whole genome breakend assembly with read pair and split read support using a probabilistic model.	Genomics Structural variation Genetic variation analysis	Sequence assembly Split-read mapping Read alignment Assembly Whole genome breakend assembly		Java	GPLv3	Cross-Platform
GRS	Reference-based data compression for storage of resequencing data		File reformatting	sequence compression	C Bourne shell	Commercial Freeware	Linux Linux 64
GSNAP	GSNAP can align both single-end and paired-end reads as short as 14 nt and of arbitrarily long length. It can detect short- and long-distance splicing, including interchromosomal splicing, in individual reads using probabilistic models or a database of known splice sites. Our program also permits SNP-tolerant alignment to a reference space of all possible combinations of major and minor alleles, and can align reads from bisulfite treated DNA for the study of methylation state.	DNA methylation RNA-Seq alignment	Read mapping Bisulfite mapping		C Perl
Hairpin Annotation	Generates a secondary structure from an RNA sequence and highlights regions of interest using RNAplot	Workflows			Java	Custom Licence	Linux 64 Windows Mac OS X
Haplowser	Haplowser: comparative haplotype browser for personal genome and metagenome		Visualisation Haplotype inference		Java	GPL
HawkEye	An interactive visual analytics tool for genome assemblies.		Sequence assembly visualisation	Sequence assembly visualisation	C++	Artistic License	Linux Mac OS X
HeliSphere	Open-source LINUX software package intended for use in analyzing data produced by the HeliScope Single Molecule Sequencer.	Whole genome resequencing Genomics SNP detection RNA-Seq	Mapping			Freeware	Linux
HI	Program for haplotype reconstruction from paired-end reads.		Haplotype reconstruction		Java
Hicup	A mapping pipeline for HiC interaction data. Performs independent mapping on each end of the interaction pair and removes commonly found artefacts.	Epigenomics	Read mapping		Perl	GPLv3	UNIX Linux Mac OS X
HINT	HMM-based Identification of TF Footprints	Epigenomics Transcription factors and regulatory sites Regulatory genomics	Peak calling Nucleic acid sequence feature detection	Digital Genomic Footprinting	Python	GPLv3	Unix-like
HiPipe	HiPipe is to make NGS data analysis quick and easy with high performance pipelines and intuitive web GUI.	Genomics	Read mapping Variant calling Workflows		JavaScript Java Bash		platform-independent
HiTEC	An algorithm which provides a highly accurate, robust, and fully automated method to correct reads produced by high-throughput sequencing methods.		Sequence error correction		C++	GPLv3	Linux
HMMSplicer	Splice junction discovery in RNA-Seq data	RNA-Seq alignment			Python
HPeak	Hidden Markov model (HMM)-based Peak-finding algorithm for analyzing ChIP-seq data to identify protein-interacting genomic regions.	ChIP-seq
HTSeq	Python framework to process and analyse high-throughput sequencing (HTS) data				Python	GPLv3
Hybrid-SHREC	Improves sequence data quality using information from multiple platforms.		Sequence error correction		Java
IBD2	Our algorithm uses a non-homogeneous hidden Markov model (HMM) that employs local recombination rates to identify chromosomal regions that are identical by descent (IBD=2) in children of consanguineous or non-consanguineous parents solely based on genotype data of siblings derived from high-throughput sequencing platforms.	Exome capture			R Java
Ibis	Ibis (Improved base identification system), is an accurate, fast and easy-to-use base caller for the Illumina sequencing system, which significantly reduces the error rate and increases the output of usable reads. Ibis is faster and makes fewer assumptions about chemistry and technology	Sequencing	Base-calling	Statistical learning of base calling parameters and calibrated quality scoring	Python C C++	Non-commercial	Linux Windows (Cygwin)
ICORN	Iteratively aligns deep coverage of short sequencing reads to correct errors in reference genome sequences and evaluate their accuracy.		Sequence assembly Sequencing quality control
IDBA	IDBA (Iterative De Bruijn graph short read Assembler) is a short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system	Sequence assembly (de novo assembly)	Sequence assembly				POSIX Linux Linux 64
IGV	The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated datasets. It supports a wide variety of data types and format, including short-read alignments in the SAM/BAM format. Data can be viewed from local files or over the web via http.	Genomics	Visualisation		Java	LGPL	Windows Mac OS X Linux
Illuminate	Analytics toolkit in Python for Illumina HiSeq and MiSeq metrics	Genomics	Sequencing quality control	object-oriented access to results of binary parsing some command line support	Python	MIT	Unix-like
Illuminator	Software for machines running Windows to identify variants in Illumina short read data.	SNP detection Indel detection
IMAGE	“Iterative Mapping and Assembly for Gap Elimination”. IMAGE closes gaps in a draft assembly using Illumina paired-end reads.		Sequence assembly editing
Inchworm	Employs the Kmer graph method to reconstruct (in many cases full-length) transcripts from Illumina RNA-Seq (preferrably strand-specific) reads.	Sequence assembly (de-novo assembly) RNA-Seq Transcriptome assembly
InGAP	inGAP is an integrated platform for next-generation sequencing project, the core function of which is to detect SNPs and indels using a Bayesian algorithm.	SNP detection	Read mapping Sequence assembly visualisation
Ingenuity Variant Analysis	Ingenuity Variant Analysis is a web application that helps researchers studying human disease to identify causal variants	Whole genome resequencing Genomics SNPs Exome	Variant classification
Integrated Genome Browser	Visualisation software for next-generation genomics	Genomics	Visualisation		Java	Open Source	platform-independent
Iobio	Real-time Genomic Analysis iobio uses immediate visual feedback to make understanding complex genomic datasets more intuitive, and analysis more interactive	Workflows	Visualisation
IOmics	iOmics is a cloud based workflow analysis framework for managing, analyzing and visualizing NGS data.	Genomics Transcriptomics ChIP-seq RNA-Seq Regulatory RNA Exome capture Epigenomics	Sequence assembly Sequence alignment Ab-initio gene prediction Variant calling MiRNA analysis Exome analysis			Commercial	cloud
IQSeq	Integrated Isoform Quantification Analysis based on A Partial Sampling Framework	RNA-Seq quantification Alternative splicing			C++
ISAAC	ISAAC comprises of genome aligner and variant caller, by Illumina.			Runtime Speed	C++		Linux 64
Isas	Fast aligner for color and base space short read data.		Sequence alignment				Linux
IsoEM	Expectation maximization algorithm for estimating alternative splicing isoform frequencies	Alternative splicing	Expectation Maximisation		Java
ISSAKE	Short Sequence Assembly by K-mer search and 3' read Extension, Immunology version (iSSAKE)	Metagenomics	Sequence assembly		Perl Python	GPLv2
JBrowse	Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse.		Visualisation		Perl JavaScript	Open Source	browser based
Jellyfish	Fast, memory-efficient k-mer counting algorithm				C++	GPLv3	Linux 64 Mac OS X
JointSLM	Copy number estimation from read depth information	Copy number estimation			R
KARMA	K-tuple Alignment with Rapid Matching Algorithm	DNA methylation Sequencing Epigenetics	Read mapping
KBASE	"KBase provides a computational framework and tools for integrating and analyzing large, diverse datasets generated by the scientific community to advance predictive understanding, manipulation, and design of biological processes in an environmental context. The purpose of KBase is to enable users to integrate a wide spectrum of genomics and systems biology data, models, and information for microbes, microbial communities, and plants. Powerful tools within KBase will allow users to analyze and simulate data to predict biological behavior, generate and test hypotheses, design new biological functions, and propose new experiments. "	Comparative genomics	Annotation				Linux
Kismeth	Web-based tool for bisulfite sequencing analysis	DNA methylation Epigenomics	Bisulfite mapping
Kissnp	kisSnp compares two sets of NGS raw reads, detecting Single Nucleotide Polymorphism occurring between the two sets. The two sets typically come from the sequencing of two individuals from the same species or from closely related species.	Transcriptomics SNP detection Indel detection Comparative genomics	Sequence assembly Sequence assembly (de-novo assembly) Data retrieval	SNP calling	C	CeCILL	Linux
Kmergenie	KmerGenie estimates the best k-mer length for genome de novo assembly. Given a set of reads, KmerGenie first computes the k-mer abundance histogram for many values of k. Then, for each value of k, it predicts the number of distinct genomic k-mers in the dataset, and returns the k-mer length which maximizes this number. Experiments show that KmerGenie's choices lead to assemblies that are close to the best possible over all k-mer lengths.	Sequence assembly	Sequence assembly		C++ Python R
KNIME	Software for organizing bioinformatic workflows		Workflows			GPLv3	Windows Mac OS X Linux
Knime4Bio	custom nodes for the interpretation of Next Generation Sequencing data with KNIME.	Genomics Transcription factors and regulatory sites Gene regulation	Data retrieval	KNIME	Java	GPLv3	any
Krona	Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).	Metagenomics	Visualisation	Interactive Animation HTML5 canvas graphics	JavaScript Perl		Linux UNIX Mac OS X
Lab7	Data workflow management platform to streamline NGS analyses	Genomics Laboratory information management	Workflows		Python JavaScript	Commercial	Mac OS X Linux
Lasergene	Lasergene is a comprehensive DNA and protein sequence analysis software suite comprised of seven applications which include functions ranging from sequence assembly and SNP detection, to automated virtual cloning and primer design.	Sequence assembly (de novo assembly) Genomics SNP detection Indel detection Mapping Transcription factors and regulatory sites Sequence analysis Phylogenetics Protein structure analysis	Sequence assembly Read mapping Sequence alignment Peak calling Annotation Sequence analysis Scaffolding Sequence alignment analysis Chromatogram visualisation PCR primer design			Commercial	Windows XP Windows 7 or Higher Mac OS X 10.7 10 8 or 10.9
LAST	Short read alignment program incorporating quality scores	Genomics Comparative genomics	Sequence alignment		C++	GPLv3
LASTZ	A tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically	Genomics	Read mapping Sequence alignment				Mac OS X Linux
LobSTR	lobSTR is an alignment and genotyping tool for profiling short tandem repeats from next generation sequencing data	Sequencing	Repeat sequence organisation analysis	Fast Scalable sequence alignment Gapped alignment	C++ R Python	Freeware	UNIX
LOCAS	LOCAS low-coverage short-read assembler		Sequence assembly		C++		Linux
LookSeq	AJAX-based browser for deep sequencing data		Sequence assembly visualisation
LSKB, Life Science Knowledge Bank	LSKB Life Science Knowledge Bank, is a comprehensive drug discovery and genomic research workbench, knowledgebase, & data management system.	Genomics	Annotation SNP calling Sequence analysis Differential expression analysis Pathway or network analysis Classification Analysis pipeline Functional analysis
MACS	Model-based Analysis of ChIP-seq data.	ChIP-seq	Peak calling		Python	Artistic License	platform-independent
MagicViewer	Large-scale short reads and sequencing depth visualization.	Sequence assembly (de novo assembly) Exome capture Genetic variation	Visualisation SNP calling		Java		platform-independent
MapDamage	Identifies and quantifies DNA damage patterns in ancient DNA	Sequencing DNA	Sequencing quality control Statistical calculation		Python R		Linux Mac OS X
MapNext	MapNext provides four mainly analysis: (i) unspliced alignment and clustering of reads, (ii) spliced alignment of transcriptomic reads, (iii) SNP detection and calculation of SNP frequency from population sequences, and (iv) storage of result data into database to make it available for more flexible query and further analyses.	RNA-Seq alignment SNP detection	Sequence alignment		C++ Perl
Mapsembler	Mapsembler is a targeted assembly software. It takes as input a set of NGS raw reads and a set of input sequences (starters). It first determines if each starter is read-coherent, e.g. whether reads confirm the presence of each starter in the original sequence. Then for each read-coherent starter, Mapsembler outputs its sequence neighborhood as a linear sequence or as a graph, depending on the user choice.	Transcriptomics Metagenomics Exome capture RNA-Seq quantification Sequencing	Sequence assembly Read mapping	De novo assembly Identify Novel Exons Remove contaminants Detect enzymes in metagenomics NGS reads	C	CeCILL	Linux
MapSplice	We introduce a second generation splice detection algorithm, MapSplice, whose focus is high sensitivity and specificity in the detection of splices as well as CPU and memory efficiency. MapSplice can be applied to both short (<75 bp) and long reads (75 bp). MapSplice is not dependent on splice site features or intron length, consequently it can detect novel canonical as well as non-canonical splices. MapSplice leverages the quality and diversity of read alignments of a given splice to increase accuracy.	RNA-Seq alignment	Mapping		C++ Python		Linux
MapView	Visualisation of short reads alignment on desktop computer		Visualisation				Linux Windows
MAQ	Mapping and Assembly with Qualities (renamed from MAPASS2). Particularly designed for Illumina-Solexa 1G Genetic Analyzer, and has preliminary functions to handle ABI SOLiD data.	Genomics SNP detection	Read mapping		C++ Perl	GPL
MAQGene	Complete pipeline for mutant discovery, with web front end	SNP detection	Read mapping Integrated solution
MARGARITA	SNP detection and genotyping from low-coverage sequencing data	SNP detection Genotyping
Mason	A fast, feature-rich and hackable read simulator for the simulation of NGS and Sanger data.	Genomics	Sequence assembly Mapping Modelling and simulation	Empirical or simple model for position dependent errors can write out sample position and extensive information about the sampled infix haplotype simulation through mutation of reference sequence.	C++	GPLv3	UNIX Windows
Mauve	Mauve Genome Alignment software, for comparing two or more draft or finished genomes	Genomics Transcriptomics	Visualisation Sequence assembly validation Sequence alignment comparison		C++ Java	GPL	Mac OS X Windows Linux
MAXIMUS	Hybrid reference and de novo assembly pipeline	Genomics	Sequence assembly
MAYDAY	Extensible platform for visual data exploration and interactive analysis and provides many methods for dissecting complex transcriptome datasets.	RNA-Seq	Visualisation
Meerkat	Meerkat is designed to identify structure variations (SVs) from paired end high throughput sequencing data.	Structural variation
MEGAN	Metagenome Analysis Software - MEGAN (âMEtaGenome ANalyzerâ) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results.	Metagenomics		metagenomic analysis functional classification		Commercial Freeware
Megraft	Megraft is a software tool to graft ribosomal small subunit (16S/18S) fragments from metagenomes onto full-length SSU sequences, enabling accurate diversity estimates from fragmentary and non-overlapping sequence data.	Metagenomics Sequence analysis Phylogenetics Community analysis Rarefaction	Sequence analysis		Perl	GPLv3	Linux UNIX Mac OS X
Meraculous	De novo genome assembler from short reads		Sequence assembly	De novo assembly scaffolding	Perl C
METAGENassist	User-friendly, web-based analytical pipeline for comparative metagenomic studies. Input can be derived from either 16S rRNA data or NextGen shotgun sequencing.	Metagenomics Machine learning	Visualisation Statistical calculation Sequence clustering	Easy-to-use point-and-click web interface; data visualization; publication-quality graphs and charts; wide variety of statistical methods; taxon-to-phenotype mapping; data filtering and normalization; supports many common input formats
Metagenome@Kin	Metagenome@Kin is an automated high throughput sequencing data analysis tool for the 16S/28S/ITS rRNA genes. It measures the composition and diversity of microbial and fungal species in natural environments.	Metagenomics	Species frequency estimation Statistical analysis
MetaSim	The software can be used to generate collections of synthetic reads.	Genomics Metagenomics	Sequence assembly Mapping Modelling and simulation		Java	Commercial Freeware
Metaxa	Metaxa uses Hidden Markov Models to identify, extract and classify small-subunit (SSU) rRNA sequences (12S/16S/18S) of bacterial, archaeal, eukaryotic, chloroplast and mitochondrial origin in metagenomes and other large sequence sets	Metagenomics Sequence analysis Phylogenetics Community analysis	Sequence analysis Hidden Markov Model		Perl	GPLv3	Linux UNIX Mac OS X
MethMarker	MethMarker facilitates the design of DNA methylation assays for COBRA, bisulfite SNuPE, bisulfite pyrosequencing, MethyLight and MSP. It also implements a systematic workflow for design, optimization and (computational) validation of DNA methylation biomarkers. This workflow starts from a preselected differentially methylated region (DMR) and results in an optimized DNA methylation assay that is ready to be tested in a large-scale clinical trial.	DNA methylation Epigenomics			Java		Windows Linux Mac OS X Solaris
Methpipe	The MethPipe software package is a computational pipeline for analyzing bisulfite sequencing data (BS-seq, WGBS and RRBS). MethPipe provides tools for mapping bisulfite sequencing read and estimating methylation levels at individual cytosine sites. Additionally, MethPipe includes tools for identifying higher-level methylation features, such as hypo-methylated regions (HMR), partially methylated domains (PMD), hyper-methylated regions (HyperMR), and allele-specific methylated regions (AMR).	DNA methylation Sequencing Epigenetics	Bisulfite mapping		C++	GPL (>= 3)	Linux Mac OS X
MethylCoder	Pipeline for fast, simple processing of BiSulfite-treated reads into methylation data. Includes scripts for analysis and visualization. In addition to a binary output, the direct output of methylcoder is a text file that indicates per-nucleotide methylation context (CG/CHG/CHH) and methylation levels (both coverage and C-T conversions)	Genomics DNA methylation Epigenomics Sequencing	Read mapping Bisulfite mapping		Python C	BSD	Linux Linux 64 Mac OS X
MetMap	Produces corrected site-specific methylation states from MethylSeq experiments and annotates unmethylated islands across the genome.	DNA methylation
MeV	Visualisation of genomic data, Differential Gene Expression based on DEGseq, DESeq and edgeR	RNA-Seq	Visualisation Differential expression analysis Sequence clustering Classification			Artistic License
MG-RAST	MG-RAST is a fully-automated service for annotating metagenome samples providing analysis tools for comparison	Metagenomics Phylogenetics Metabolic reconstruction	Annotation		Perl C GO JavaScript Python		UNIX
MicroRazerS	MicroRazerS is a tool optimized for mapping short RNAs onto a reference genome.		Read mapping		C++		Linux
Microsoft Biology Foundation	C#/.NET library for biological applications.				C#
MICSA	Combines positional information with information on motif occurrences to better predict binding sites of transcription factors (TFs)	ChIP-seq Sequence motifs	Sequence motif comparison
Minia	De novo assembly of human genomes on a desktop computer	Sequence assembly (de novo assembly)	Sequence assembly	Memory efficient and fast	C++	CeCILL	Linux Mac OS X
MIP Scaffolder	MIP Scaffolder is a program for scaffolding contigs produced by fragment assemblers using mate pair data.		Scaffolding		C++ Perl		Linux
MIRA	MIRA 3 - Whole Genome Shotgun and EST Sequence Assembler	Sequence assembly (de novo assembly) RNA-Seq alignment SNP detection	Sequence assembly Read mapping Local sequence alignment K-mer counting Graph reduction Learning algorithm		C++	GPL	Linux Mac OS X UNIX
MiRanalyzer	Web-server for identifying and analyzing miRNA in next-gen sequencing experiments	Regulatory RNA		Annotation of micro RNA differential expression	Java Perl		browser based
MiRCat	Predicts mature miRNAs and their precursors from an sRNA dataset and a genome.	Workflows	MicroRNA detection	Detection and prediction of known or novel miRNAs secondary structure generation	Java	Custom Licence	Linux 64 Windows Mac OS X
MiRDeep	Discovering known and novel miRNAs from deep sequencing data	Regulatory RNA			Perl
MiRNAkey	A software pipeline for the analysis of microRNA Deep Sequencing data	Regulatory RNA			Java Perl		Linux Mac OS X
MiRProf	Determines normalised expression levels of sRNAs matching known miRNAs in miRBase.	Workflows	MicroRNA detection		Java	Custom Licence	Linux 64 Windows Mac OS X
MiRspring	missing				Perl JavaScript	GNU
MirTools	Web server for microRNA profiling and discovery based on high-throughput sequencing	Transcriptomics Regulatory RNA			Perl PHP
MirTrios	mirTrios is a web server to accurately detect de novo mutations (DNMs) based on Expectation-maximization (EM) model. mirTrios also surports identification of rare inherited mutations, known diagnostic variants, as well as the prioritisation of novel and promising candidate genes.	Genomics Sequence analysis De novo mutation detection	Read mapping Variant calling De novo mutation detection		Perl PHP JavaScript		Linux
MISO	An alternative to Cufflinks, MISO (Mixture-of-Isoforms) is a probabilistic framework that quantitates the expression level of alternatively spliced genes.	RNA-Seq RNA-Seq quantification Alternative splicing
Mlgt	Processing and analysis of high throughput, long-read (e.g. Roche 454) sequences generated from multiple loci and multiple biological samples. Sequences are assigned to their locus and sample of origin, aligned and trimmed. Where possible, genotypes are called and variants mapped to known alleles.	Exome capture Genotyping Resequencing	Sequence error correction Sequence contamination filtering Sequence analysis Read alignment DNA barcoding	Sequence assignment sequence alignment allignment error correction variant counting genotype calling allele-matching	R	GPL >=2	Windows UNIX Mac OS X
MMSEQ	Pipeline and methodology for simultaneously estimating isoform expression and allelic imbalance in diploid organisms using RNA-seq data.	DNA transcription			C++		Mac OS X Linux 64
MochiView	Hybrid genome browser and motif visualization/analysis/management desktop software.	Genomics ChIP-seq RNA-Seq ChIP-on-chip Sequence motifs	Genome visualisation Sequence motif comparison	Desktop hybrid genome browser and motif visualization/analysis software	Java		Linux Mac OS X Windows
MoDIL	Program to detect small indels in next generation sequencing data	Genomics Indel detection			Python
MOM	Short-read mapping	Genomics	Read mapping
MOSAIK	Reference guided aligner/assembler.		Sequence assembly		C++	Commercial GPLv2	Windows Linux Mac OS X
MotifLab	MotifLab is a general workbench for analysing regulatory sequence regions and discovering transcription factor binding sites and cis-regulatory modules within a rich graphical interface.	ChIP-seq Sequence motifs Transcription factors and regulatory sites Sequence analysis Gene regulation	Visualisation Peak calling Genome visualisation Sequence contamination filtering Sequence motif discovery Format conversion	Complete motif discovery workbench: import DNA sequences and download additional data tracks from UCSC Genome Browser visualize tracks in the integrated genome browser perform de novo motif discovery or search for instances of known motifs use operations to pre- and post-process data tracks explore the data interactively with various analysis tools automatically record all your steps in protocols that can be executed as workflows	Java	Freeware	platform-independent
MPscan	MPscan (multi-pattern scan) is a program for mapping short reads (<30bp) exactly on a set of reference sequences (eg, a genome) without indexing the reference. MPscan performs only exact mapping (no substitution, nor indels), is fast (optimal complexity), and easy to use.	Genomics Transcriptomics	Read mapping		C++		Linux Mac OS X
MrBayes	"MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters."	Phylogenetics	Statistical calculation				Cross-Platform
MrCaNaVaR	mrCaNaVaR is a copy number caller that analyzes the next-generation sequence mapping read depth to discover large segmental duplications and deletions. It also has the capability of predicting absolute copy numbers of genomic intervals.	Genomics Personalised medicine Copy number estimation	Read depth analysis		C	Commercial Freeware	POSIX
MrFAST	mrFAST is designed to map short reads generated with the Illumina platform to reference genome assemblies; in a fast and memory-efficient manner.	Genomics Read alignment	Read alignment		C	BSD	UNIX
MrsFAST	mrsFAST is a micro-read substitution-only Fast Alignment Search Tool. mrsFAST is a cache-oblivous short read mapper that optimizes cache usage to get higher performance.	Genomics	Mapping Read alignment		C	BSD	UNIX
MTR	Metagenomics software for clustering at multiple ranks.	Metagenomics			C++ Matlab
MU2A	Genomic variant annotation tool	SNP	SNP annotation		Java	Apache License 2.0	Windows Linux Mac OS X
MultiPSQ	MultiPSQ expedites the analysis and evaluation of multiplex-pyrograms, generated from multiplex pyrosequencing	Phylogenetics Microbial Surveillance Public health and epidemiology	Peak calling Classification Peptide mass fingerprint		C++	LGPLv3	Windows Linux
MultiQC	MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.	Next Generation Sequencing	Quality control	Data Visualisation	Python	GPLv3	Windows Mac OS X Linux
MUMmer	MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. Basically it is a ultra-fast alignment of large-scale DNA and protein sequences	Genomics Transcriptomics	Read mapping Sequence alignment			Artistic License	Linux
MUMmerGPU	MUMmerGPU is a low cost, ultra-fast sequence alignment program designed to handle the increasing volume of data produced by HTS.	Genomics Transcriptomics	Sequence alignment
MuMRescueLite	Probabilistically reincorporates multi-mapping tags into mapped short read data.	Genomics ChIP-seq	Mapping		Python	MIT
MuSICA 2	Assembles millions of short (36-nucleotide) reads collected from a single flow cell lane of Illumina Genome Analyzer to shotgun-sequence ~800 human full-length cDNA clones.	Clone verification	Sequence assembly		Perl
Mutascope	Mutascope is a software suite designed to analyze data from high throughput sequencing of PCR amplicons, with an emphasis on normal-tumor comparison for the accurate and sensitive identification of low prevalence mutations.	Cancer biology	Variant calling Analysis pipeline		Perl		UNIX
MuTect	MuTect is a method developed at the Broad Institute for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes.		SNP calling
Myrialign	Software to align short reads produced by a short read genome sequencer to a reference genome. Alignments can contain any number of SNPs, insertions and deletions, up to a user specified cutoff. Myrialign can use a Cell Broadband Engine processor to accelerate alignments if available, for example on a PlayStation 3 running GNU/Linux. Myrialign performs brute force alignment using a variant on the "bitap" algorithm that aligns several thousand reads to a reference in parallel. It uses bit-parallelism, multiple processors, and Cell SPUs if available. Unlike other reference genome alignment software, heuristics and hashtable lookups are not used. Myrialign will find alignments with any number of errors up to a user specified cutoff. The emphasis is on doing a 100% accurate search as fast as is possible.		Read mapping Sequence alignment
Myrna	Myrna is a cloud computing tool for calculating differential gene expression in large RNA-seq datasets.	RNA-Seq alignment RNA-Seq quantification
Mzip	Reference-based sequence data compression tool		File reformatting
NarrowPeaks	Analysis of variation in ChIP-seq using functional PCA	ChIP-seq	Peak calling Differential Binding	R/Bioconductor package can run on major computer platforms	R	Artistic-2.0	Linux Mac OS X Windows
NCBI Genome Workbench	"NCBI Genome Workbench is an integrated application for viewing and analyzing sequence data. With Genome Workbench, you can view data in publically available sequence databases at NCBI, and mix this data with your own private data."	Sequencing Sequence analysis Sequence annotation Next Generation Sequencing	Visualisation Genome visualisation				Cross-Platform
Nephele	NIAID, a cloud based tool for microbiome or metagenomics data analysis. Nephele allows you to process and analyze 16S raw data using pipelines based on QIIME and mothur. It also facilitates WGS functional analyses using bioBakery tools such as MetaPhlAn, HUMMAnN and metagenomic assembly using the a5-miseq/UDBA-UD.	Metagenomics Microbial Ecology Microbiome	Functional analysis Taxonomic profiling Metagenomic Assembly	Pipelines
Nesoni	Nesoni is a high-throughput sequencing data analysis toolset.	RNA-Seq alignment SNP detection Phylogenetics	Sequence alignment	largely for bacterial genomes	Python
Newbler	The assembly/mapping program developed by 454 Life Sciences for of 454 data	Sequence assembly (de novo assembly)	Sequence assembly Read mapping		C++	Unknown	Linux 64
Nexalign	Nexalign is a program to align millions of short reads from next-generation sequencing data sets to reference genomes		Read mapping		C++ R	GPL	UNIX
NextGen Utility Scripts	A collection of links to scripts available for working with data generated by new sequencing technologies.			A collection of many different scripts
NextGENe	de novo and reference assembly of Roche/454, Illumina and SOLiD data. Uses a novel Condensation Assembly Tool approach where reads are joined via "anchors" into mini-contigs before assembly which reduces sequencing errors. Requires Win or MacOS.	Sequence assembly (de novo assembly) SNP detection Indel detection Metagenomics Exome capture		Unique condensation tool Data Visualisation very flexible	C++	Commercial	Windows
Ngs backbone	ngs_backbone is a bioinformatic application created to work on sequence analysis by using NGS (Next Generation Sequencing) and sanger sequences. It is capable of cleaning reads, do de novo assembly or mapping against a reference and annotate SNPs, SSRs, ORFs, GO terms and sequence descriptions.	Genomics SNP detection	Sequence assembly Read mapping			AGPL	UNIX
NGS-DesignTools	Tools to assist in designing deep sequencing experiments for haplotype reconstruction and structural variant breakpoint detection	RNA-Seq quantification Structural variation	Haplotype inference Modelling and simulation
Ngs-pipeline	Complete solution for human re-sequencing projects	SNP detection Indel detection Epigenomics Structural variation Personalised medicine	Read mapping Sequence annotation		Perl	GPLv3	Linux
Ngs.plot	ngs.plot is a program that allows you to easily visualize your next-generation sequencing (NGS) samples at functional genomic regions. The signature advantage of ngs.plot is that it collects a large database of functional elements for many genomes. A user can ask for a functionally important region to be displayed in one command. It handles large sequencing data efficiently and has only modest memory requirement. A web-based version (integrated into Galaxy) is also available for the ones who are allergic to terminals.	Transcriptomics Epigenomics	Visualisation	Data Visualisation	R Python	GPL (>= 3)	All
NGSUtils	NGSUtils is a suite of software tools for working with next-generation sequencing datasets	Genomics Transcriptomics	Formatting Sequencing quality control Sequence contamination filtering Variant calling Read pre-processing		Python	GPL	Linux Mac OS X
NGSView	High-throughput sequencing technologies introduce novel demands on tools available for data analysis. We have developed NGSView, a generally applicable, flexible and extensible next-generation sequence alignment editor. The software allows for visualization and manipulation of millions of sequences simultaneously on a desktop computer, through a graphical interface. NGSView is available under an open source license and can be extended through a well documented API.	Genomics	Sequence assembly visualisation
NOISeq	Next Generation Sequencing (NGS) technologies are increasingly being used for gene expression pro�filing as a replacement for microarrays. The expression level given by these technologies is the number of reads in the library mapping to a given feature (gene, exon, transcript, etc.), i.e., the read counts. Most of the statistical methods for assessment of differential expression using count data rely on parametric assumptions about the distribution of the counts (Poisson, Negative Binomial, …). Moreover, many of them need replicates to work and tend to have problems to evaluate differential expression in features with low counts. NOISeq is a non-parametric approach for the identification of differentially expressed genes from count data. NOISeq empirically models the noise distribution of count changes by contrasting fold-change differences (M) and absolute expression differences (D) for all the features in samples within the same condition. This reference distribution is then used to assess whether the M-D values computed between two conditions for a given gene is likely to be part of the noise or represent a true differential expression. The are two variants of the method: NOISeq-real uses replicates, when available, to compute the noise distribution and, NOISeq-sim simulates them in absence of replication. It should be noted that the NOISeq-sim simulation procedure assimilates to technical replication and does not reproduce biological variability, which is necessary for population inferential analysis.	Gene expression	Differential expression analysis
NovelSeq	A computational framework to discover the content and location of long novel sequence insertions using paired-end sequencing data	Indel detection Structural variation	Sequence assembly Read mapping Variant calling		C	BSD	UNIX
Novocraft	Novoalign is a program for mapping short reads from the Illumina/SOLiD sequencing platform(s) to a reference genome.	Whole genome resequencing Genomics ChIP-seq RNA-Seq alignment Regulatory RNA	Read mapping	Bisulfite sequencing Mate-pair/jumping libraries parallel execution insertions/deletions SAM format output paired-end colourspace MPI	C++	Commercial Freeware	Mac OS X Linux 64
NPS	Identify nucleosome positions given histone-modification ChIP-seq or nucleosome sequencing at the nucleosome level.	ChIP-seq Epigenomics			Python
NucleR	nucleR is a R/Bioconductor package for working with tiling arrays and next generation sequencing. It uses a novel aproach in this field which comprises a deep profile cleaning using Fourier Transform and peak scoring for a quick and flexible nucleosome calling	ChIP-seq Epigenomics ChIP-on-chip DNA packaging	Peak calling Annotation	Multicore Integrated solution	R	LGPLv3	Cross-Platform
Oases	De novo transcriptome assembler for very short reads	Sequence assembly (de-novo assembly) Transcriptome assembly		supports strand specific and paired-end RNA-seq data sets	C	GPLv3
Oasis	Oasis is a web application that allows for the fast and flexible online analysis of small-RNA-seq (sRNA-seq) data. It was designed for the end user in the lab, providing an easy-to-use web frontend including video tutorials, demo data, and best practice step-by-step guidelines on how to analyze sRNA-seq data. Oasis' exclusive selling points are a differential expression module that allows for the multivariate analysis of samples, a classification module for robust biomarker detection, and an API that supports the batch submission of jobs. Both modules include the analysis of novel miRNAs, miRNA targets, and functional analyses including GO and pathway enrichment. Oasis generates downloadable interactive web reports for easy visualization, exploration, and analysis of data on a local system.	RNA	Read mapping Differential expression analysis	differential expression classification API miRNA target prediction	JavaScript Perl Java Python Bash C		all supporting JVM
ODIN	ODIN is an HMM-based approach to detect and analyse differential peaks in pairs of ChIP-seq data.	Genomics Regulatory genomics	Peak calling		Python		tested for Linux (Ubuntu)
OLego	OLego is a program specifically designed for de novo spliced mapping of mRNA-seq reads. OLego adopts a seeding and extension scheme, and does not rely on a separate external mapper. It achieves high sensitivity of junction detection by using very small seeds (12-14 nt), efficiently mapped using Burrows-Wheeler transform (BWT) and FM-index. This also makes it particularly sensitive for discovering small exons. It is implemented in C++ with full support of multiple threading, to allow fast processing of large-scale data.	Genomics RNA-Seq alignment RNA-Seq	Read mapping Sequence alignment	capable of using very small seeds for splice Read mapping but still fast and accurate	C++	GPLv3	Linux Linux 64 Mac OS X
Omixon Variant Toolkit	Omixon Target Standard, Target HLA and Target Pro are designed to help clinical, diagnostic and research labs to efficiently get the maximum accuracy and precision from their targeted NGS data.	SNP detection Indel detection Mapping Sequence analysis Comparative genomics	Sequence assembly Read mapping Sequence alignment	easy to use parameters full documentation also a plugin available in CLCbio and Geneious		Commercial Freeware	interoperable
Optimus Primer	Automated primer design for large-scale resequencing by second generation sequencing	Resequencing	PCR primer design
PacBio conversion tools	Tools to convert from PacBio HDF5 format to other commonly used formats & libraries to read HDF5 from Java & R		File reformatting		Java R Python
PaCGeE	PaCGeE (Parallel Computational Genomics Engine) is a suite of HPC accelerated sequence data analysis tools for assembly and analysis. The tool set comprises of many popular open source and proprietary software for a high performance, high throughput and high quality data analysis. The PaCGeE family of parallel NGS analysis tools are Cloud-MAQ, VELVET-P, EULER, ERANGE, BOWTIE, BFAST, MPI-BLAST, ChIP Seq Peak Finder etc		Read mapping			Commercial
PALMA	We present a novel approach based on large margin learning that combines accurate splice site predictions with common sequence alignment techniques. By solving a convex optimization problem, our algorithm -- called PALMA -- tunes the parameters of the model such that true alignments score higher than other alignments. We study the accuracy of alignments of mRNAs containing artificially generated micro-exons to genomic DNA. In a carefully designed experiment, we show that our algorithm accurately identifies the intron boundaries as well as boundaries of the optimal local alignment. It outperforms all other methods: for 5702 artificially shortened EST sequences from C. elegans and human it correctly identifies the intron boundaries in all except two cases. The best other method is a recently proposed method called exalin which misaligns 37 of the sequences. Our method also demonstrates robustness to mutations, insertions and deletions, retaining accuracy even at high noise levels.	RNA-Seq alignment	Sequence alignment
PALMapper	Fast and Accurate Spliced Alignments of Sequence Reads.		Read mapping		C++	GPLv3
PanGEA	Tool which enables a fast and user-friendly analysis of allele specific gene expression using the 454 technology.	SNP detection RNA-Seq DNA transcription			Perl	Mozilla Public License
PARalyzer	Tool to analyze cross-linking and immunoprecipitation data (CLIP)				Java	Commercial Freeware
Partek Genomics Suite	Easy to use software providing A to Z analysis for all Next Generation Sequencing and Microarray data.	Transcriptomics ChIP-seq SNP detection RNA-Seq quantification DNA transcription Epigenomics Alternative splicing Functional genomics
PASH	Pash 3.0 performs sequence comparison and read mapping and can be employed as a module within diverse configurable analysis pipelines, including ChIP-seq and methylome mapping by whole-genome bisulfite sequencing	DNA methylation Epigenomics	Sequence alignment Bisulfite mapping
PASS	PASS performs fast gapped and ungapped alignments of short DNA sequences onto a reference DNA, typically a genomic sequence. It is designed to handle a huge amount of reads such as those generated by Solexa, SOLiD or 454 technologies. The algorithm is based on a data structure that holds in RAM the index of the genomic positions of seed" words (typically 11-12 bases) as well as an index of the precomputed scores of short words (typically 7-8 bases) aligned against each other.		Sequence alignment		C++		Linux Windows
Patchwork	Patchwork is a bioinformatic tool for analyzing and visualizing allele-specific copy numbers and loss-of-heterozygosity in cancer genomes. The data input is in the format of whole-genome sequencing data which enables characterization of genomic alterations ranging in size from point mutations to entire chromosomes. High quality results are obtained even if samples have low coverage, ~4x, low tumor cell content or are aneuploid. Patchwork is available in two formats. The first, named simply patchwork, takes BAM files as input whereas patchworkCG takes input from CompleteGenomics files. Detailed guides and information regarding these can be found in their respective tabs.	Structural variation Copy number estimation		Allele specific copy numbers.	R		Linux Mac OS X
PatMaN	Patman searches for short patterns in large DNA databases, allowing for approximate matches. It is optimized for searching for many small pattern at the same time, for example microarray probes.		Read mapping
PE-Assembler	A simple 3' extension approach to assembling paired-end reads and capable of parallelization	Sequence assembly (de novo assembly)	Scaffolding		C++
PeakAnalyzer	PeakAnalyzer is a set of applications for processing ChIP signal peaks.	ChIP-seq Functional genomics			Java C++ R
PeakRanger	A multi-purpose, ultrafast ChIP Seq peak caller	ChIP-seq	Peak calling		C++	Artistic License	Linux Mac OS X
PeakSeq	PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. A methodology for identifying punctate binding sites in ChIP-seq experiments based on their characteristics. publication	ChIP-seq			C Perl
PeakTrace	PeakTrace is an alternative basecaller for improving the quality and read length of Sanger DNA sequencing traces. The PeakTrace basecaller works with trace files produced by the ABI 310, 3700, 3100, 3130, 3730, and 3500 DNA sequencers. MegBACE sequencers are also supported.	Sequencing	Base-calling	DNA basecaller	C	Commercial	Windows Mac OS X Linux 64
PECAN	Alignment method practical for large genomic sequences.		Sequence alignment
PEMer	The package is composed of three modules, PEMer workflow, SV-Simulation and BreakDB. PEMer workflow is a sensitive software for detecting SVs from paired-end sequence reads. SV-Simulation randomly introduces SVs into a given genome and generates simulated paired-end reads from the ‘novel’ genome. Subsequent analysis with PEMer workflow on the simulated reads can facilitate parameterize PEMer workflow. BreakDB is a web accessible database developed to store, annotate and dsplay SV breakpoint events identified by PEMer and from other sources.	Structural variation
PERalign	A probabilistic framework is described to predict the alignment to the genome of all paired-end read transcript fragments in a paired-end read dataset. Starting from possible exonic and spliced alignments of all end reads, our method constructs potential splicing paths connecting paired ends. An expectation maximization method assigns likelihood values to all splice junctions and assigns the most probable alignment for each transcript fragment.	RNA-Seq alignment			C++		Linux
PerM	PerM (Periodic Seed Mapping) uses periodic spaced seeds to significantly improve mapping efficiency for large reference genomes when compared to state-of-the-art programs.	Genomics SNP detection	Read mapping		C++	Apache License 2.0	Linux
Phred	The phred software reads DNA sequencing trace files, calls bases, and assigns a quality value to each called base.		Base-calling		C		Solaris IRIX AIX
Phred Phrap Consed Cross match	The phred software reads DNA sequencing trace files, calls bases, and assigns a quality value to each called base. Phrap is a program for assembling shotgun DNA sequence data. Cross_match is a general purpose utility for comparing any two DNA sequence sets using a 'banded' version of swat. Consed/Autofinish is a tool for viewing, editing, and finishing sequence assemblies created with phrap.		Sequence assembly Sequence alignment Base-calling Local sequence alignment
Phymm	A classifier for metagenomic data, that has been trained on 539 complete, curated genomes and can accurately classify reads as short as 100 base pairs	Metagenomics
PiCall	Identifies short indel polymorphisms in population sequencing data	Indel detection Population genetics			C
PICS	PICS identifies binding event locations by modeling local concentrations of directional reads, and uses DNA fragment length prior information to discriminate closely adjacent binding events via a Bayesian hierarchical t-mixture model.	ChIP-seq			R
PileLine	PileLine is a flexible command-line toolkit for efficient handling, filtering, and comparison of genomic position (GP) files produced by next-generation sequencing experiments. PileLineGUI adds a graphical interface.		Plotting and rendering		Java	LGPL
Pindel	A pattern growth approach to detect break points of large deletions and medium sized insertions from paired end short reads.	Indel detection Structural variation	Read mapping Split-read mapping Localised reassembly		C++		Linux Mac OS X Windows
Pipeline Pilot	Analysis and workflow development of Next Generation Sequencing and gene expression.	Sequence assembly (de novo assembly) Whole genome resequencing Genomics ChIP-seq SNP detection RNA-Seq Sequence analysis Gene expression analysis Next Generation Sequencing	Read mapping Sequence alignment Sequence analysis Variant calling Comparative genomics Gene expression analysis	Integrated solution wrapping custom and third party tools for integration analysis and reporting	C++ Java Perl R Pilot Script	Commercial	Linux Windows
PIQA	PIQA is a quality analysis pipeline designed to examine genomic reads produced by Next Generation Sequencing technology (Illumina G1 Genome Analyzer). It is a set of libraries for R.		Sequencing quality control		R
PoissonSeq	Identify differential expressed genes	Gene expression	Differential expression analysis
PolyBayesShort	A re-incarnation of the PolyBayes SNP detection tool developed by Gabor Marth at Washington University. This version is specifically optimized for the analysis of large numbers (millions) of high-throughput next-generation sequencer reads, aligned to whole chromosomes of model organism or mammalian genomes. Developers at Boston College.	SNP detection					Linux Linux 64
PoolHap	Computational tool for inferring haplotype frequencies from pooled samples when haplotypes are known. In future version, haplotype unknown analysis will be supported.		Read mapping Regression analysis
PoPoolation	Toolbox specifically designed for the population genetic analysis of sequence data from pooled individuals.	Population genetics			Perl R
PoPoolation2	PoPoolation2 allows to compare allele frequencies for SNPs between two or more populations and to identify significant differences. PoPoolation2 requires next generation sequencing data of pooled genomic DNA (Pool-Seq). It may be used for measuring differentiation between populations, for genome wide association studies and for experimental evolution.	Genomics Population genetics			Perl R
Post Assembly Genome Improvement Toolkit	" Tools to generate automatically high quality sequence by ordering contigs, closing gaps, correcting sequence errors and transferring annotation. With the advent of next generation sequencing a lot of effort was put into developing software for mapping or aligning short reads and performing genome assembly. For genome assembly the problem of generating a draft assembly (i.e. a set of unordered contigs) has now been very well addressed - but for users who need high quality assemblies for their analyses there are still unresolved issues: this is where PAGIT is used. "	Sequence assembly (de novo assembly)	Sequence assembly validation				Linux
Precrec	Precrec is a CRAN package that provides accurate computations of ROC and Precision-Recall curves.				R	GPL-3	Windows Mac OS X Unix-like
PRICE	PRICE uses paired-read information to iteratively increase the size of existing contigs.		Sequence assembly		C++
PRINSEQ	PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions.	Genomics Transcriptomics Metagenomics	Sequence contamination filtering Sequence trimming Read pre-processing		Perl	GPLv3	UNIX Mac OS X Windows
ProbeMatch	Matches a large set of oligonucleotide sequences against a genome database using gapped alignments		Mapping				Linux Mac OS X
ProbHD	We present a new strategy for identifying heterozygous sites in a single individual by using a machine learning approach that generates a heterozygosity score for each chromosomal position. Our approach also facilitates the identification of regions with unequal representation of two alleles and other poorly sequenced regions. The availability of confidence scores allows for a principled combination of sequencing results from multiple samples.	SNP detection Population genetics			Perl R Python
Promisec Endpoint Manager	Promisec Endpoint Manager 2.41 uses patented, agentless technology to quickly and remotely inspect yan organisations endpoint environment to discover, analyze, and remediate any abnormalities that then in turn lead to failed audits and uncorrect business intelligence.		Security Endpoint Management Remediation
Proxygenes	We introduce a clustering method which significantly reduces the size of a metagenome dataset while maintaining a faithful representation of its functional and taxonomic content.	Metagenomics	Read mapping Annotation
Pybedtools	Python extension to BEDTools that allows use of all BEDTools programs directly from Python, as well as feature-by-feature manipulation, automatic handling of temporary files, and more.	Genomics	Read mapping	See full description	Python	GPLv2	Windows (Cygwin) Linux Linux 64 Mac OS X
PyroBayes	PyroBayes is a novel base caller for pyrosequences from the 454 Life Sciences sequencing machines.	SNP detection	Base-calling
PyroMap	PyroMap accurately maps pyrosequencing reads onto reference sequences using a selectively weighted Smith-Waterman (SW^2) algorithm to incorporate quality scores into alignment.		Read mapping		Python
PyroNoise	Clustering of pyrosequencing (454) data with noise model (AmpliconNoise) and chimaera removal (Perseus) for sequence diversity analysis.	Metagenomics Phylogenetics
QCALL	SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples	SNP detection
Qpalma	QPalma is an alignment tool targeted to align spliced reads produced by Next Generation sequencing platforms	RNA-Seq alignment	Sequence alignment		Python C++
QRidge	Given a set of RNA-Seq data, QRidge assembles the short reads into long full-length transcripts.	Sequence assembly (de-novo assembly) Transcriptome assembly	Sequence assembly
QSeq	QSeq is DNASTAR's Next-Gen application for RNA-Seq, ChIP-seq, and miRNA alignment and analysis.	ChIP-seq RNA-Seq Regulatory RNA	Sequence alignment Visualisation Peak calling			Commercial	Windows 7 64-bit or Higher Mac OS X 10.7 10.8 or 10.9 with Parallels Desktop
QSRA	Quality-value guided Short Read Assembler, created to take advantage of quality-value scores as a further method of dealing with error. Compared to previous published algorithms, our assembler shows significant improvements not only in speed but also in output quality.	Sequence assembly (de novo assembly)	Sequence assembly
QuadGT	QuadGT is a software package for calling single-nucleotide variants in four sequenced genomes: normal-tumor pairs coupled with parents. Genotypes are inferred using a joint model of parental variant frequencies, de novo germline mutations, and somatic mutations. The model quantifies the descent-by-modification relationships between the unknown genotypes by using a set of parameters in a Bayesian inference setting.	SNPs	SNP calling Variant calling		Java
Quake	Program to detect and correct errors in DNA sequencing reads. Using a maximum likelihood approach incorporating quality values and nucleotide specific miscall rates,		Sequence error correction
QualiMap	Qualimap is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data.		Sequencing quality control		Java R
QUAST	QUAST stands for QUality ASsessment Tool. It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.	Sequence assembly Data handling	Visualisation Sequence assembly validation	Data Visualisation Assembly Quality Evaluation Detailed Reports	Python C Perl	GPLv2	Linux Mac OS X
QuEST	QuEST is a Kernel Density Estimator-based package for analysis of massively parallel sequencing data from chromatin immunoprecipitations (ChIP-seq or ChIPseq).	ChIP-seq			C++	GPLv2
Quip	Aggressive compression of FASTQ and SAM/BAM files.		File reformatting		C	BSD (3-clause)	any
R2R	R2R is a simple to use package for very sensitive analysis of short read sequence data obtained by NextGen sequencing techniques. R2R was developed in conjunction with data obtained on the Illumina GA platforms. R2R is written in simple Perl script and runs equally well under MS Windows, Mac OS and Linux/Unix operative systems.	SNP detection	Sequence alignment		Perl
R453Plus1Toolbox	Facilitates analysis of data from 454 sequencer in R/Bioconductor.				R
RACA	Reference-Assisted Chromosome Assembly (RACA)
RApiD	Tools for processing restriction site associated DNA sequencing.	SNP detection			Perl C++	GPLv3
RAPSearch	Fast protein similarity search tool for short reads that utilizes a reduced amino acid alphabet and suffix array to detect seeds of flexible length.	Metagenomics	Sequence alignment		C++	GPLv3
RAST	"RAST (Rapid Annotation using Subsystem Technology) is a fully-automated service for annotating complete or nearly complete bacterial and archaeal genomes. It provides high quality genome annotations for these genomes across the whole phylogenetic tree."	Genomics Phylogenetics	Genomics Annotation
Ray	de novo genome assembly is now a challenge because of the overwhelming amount of data produced by sequencers. Ray assembles reads obtained with new sequencing technologies (Illumina, 454, SOLiD) using MPI 2.2 -- a message passing inferface standard.	Sequence assembly (de novo assembly)	Sequence assembly	MPI 2.2 de Bruijn graphs parallel Illumina data	C++	GPL	Linux POSIX
RazerS	RazerS allows the user to align sequencing reads of arbitrary length using either the Hamming distance or the edit distance. The tool can work either lossless or with a user-defined loss rate at higher speeds.	Mapping	Read mapping Local sequence alignment	Gapped alignment paired-end mapping	C++	GPLv3	UNIX Mac OS X Windows
RDiff	rDiff is an open source tool for accurate detection of differential RNA processing from RNA-Seq data. It implements two statistical tests to detect changes of the RNA processing between two samples. rDiff.parametric is a powerful test, which can be applied for well annotated organisms to detect changes in the relative abundance of isoforms. rDiff.nonparametric is an alternative when the annotation is incomplete or missing.	Transcriptomics RNA-Seq Alternative splicing	Sequence alignment Differential expression analysis		Python Matlab	Open Source	Linux Mac OS X
RDP Pyrosequencing Pipeline	The Ribosomal Database Project's Pyrosequencing Pipeline aims to simplify the processing of large 16s rRNA sequence libraries obtained through pyrosequencing. This site processes and converts the data to formats suitable for common ecological and statistical packages such as SPADE, EstimateS, and R.	Metagenomics	Sequence alignment Formatting				browser based
Readaligner	A tool for mapping (short) DNA reads into reference sequences.		Read mapping
ReadDepth	Detects copy number aberrations in deep sequencing data	Copy number estimation			R	Apache License 2.0
REAL	REad ALigner for Next-Generation sequencing reads		Mapping		C++	GPLv3	Linux
Reaper	Reaper is a program for demultiplexing, trimming and filtering short read sequencing data.	Next Generation Sequencing	Adapter removal Sequencing quality control Sequence contamination filtering Sequence trimming DNA barcoding	Memory efficient and fast.	C	GPLv3	Linux UNIX Mac OS X
... further results