Software/list

For breakdowns and stuff see...

	Summary text	Biological category	Method category	Created by
.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
4peaks	Allows viewing sequencing trace files, motif searching trimming, BLAST and exporting sequences.	Sequencing	Sequence analysis	mekentosj
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	Andrew Tritt Jonathan A. Eisen Marc T. Facciotti Aaron E. Darling
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	ABI
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	ABI
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
ABMapper	Maps RNA-Seq reads to target genome considering possible multiple mapping locations and splice junctions	Genomics Transcriptomics	Read mapping Sequence alignment	Shaoke Lau
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)	Simpson J Jackman S Birol I
Adapter Removal (software)	Removes adaptor fragments from raw short read sequence data and outputs data to FASTA format.	Workflows	Adapter removal	Stocks MB Mapleson D Moxon S
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	Kaushalya Amarasinghe
AGE	AGE is a tool that implements an algorithm for optimal alignment of sequences with SVs.	Structural variation	Sequence alignment
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	Sanchit Misra Ankit Agrawal Wei-keng Liao Alok Choudhary
Agp2amos	missing		Formatting
Alcovna	ALgorithms for COmparing and Visualizing Non Assembled data	SNP detection
ALEXA-Seq	Alternative Expression Analysis by massively parallel RNA sequencing	RNA-Seq quantification Alternative splicing
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	Pop M
ANCHOR	Post-processing tools for de novo assemblies	De-novo assembly	Sequence assembly
AnCorr	Webserver/tool for evaluation coordinate and ordinal correlations between genomic tracks and/or expression or protein binding profiles.	Genomics	Statistical calculation Correlation	Kravatsky YV Chechetkin VR Kravatskaya GI
Anno-J	Annotation Browsing 2.0	Sequencing	Visualisation	Julian Tonti-Filippini
ANNOVAR	ANNOVAR: Functional annotation of genetic variants from high-throughput sequencing data	Genomics Genetics	Annotation Variant prioritisation	Kai Wang
Arachne	ARACHNE is a program for assembling data from whole genome shotgun sequencing experiments.		Sequence assembly	Batzoglou S Jaffe DB Stanley K Butler J Gnerre S Mauceli E Berger B Mesirov JP Lander ES
AREM	AREM: Aligning Short Reads from ChIP-sequencing by Expectation Maximisation	ChIP-seq	Read mapping Peak calling	Daniel Newkirk Jacob Biesinger Alvin Chon
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	Omicsoft Corporation
ArrayExpressHTS	R-based pipeline for RNA-Seq data analysis.	RNA-Seq RNA-Seq quantification
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
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	Walenz B Florea L Mobarry C Sutton G
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	Fuli Yu Danny Challis Jin Yu Uday Evani
Atlas-SNP2	Atlas-SNP2 is a SNP detection tool developed for next generation sequencing platforms	SNP detection
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	Yeshodari
Baa.pl	use transcripts to assess a de novo assembly	Sequence assembly (de novo assembly)	Sequence assembly validation Sequence alignment analysis	Ryan JF
Bambino	Variant detector and graphical alignment viewer for SAM/BAM format data.	SNP detection Genetic variation
Bambus	Bambus is a general purpose scaffolder		Scaffolding	Koren S Pop M
BAMseek	BAMseek is a large file viewer for BAM and SAM alignment files.	Genomics Transcriptomics	Sequence alignment visualisation	BAMseek
BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.		Sequence alignment analysis	Derek Barnett
BamView	Interactive Java application for visualising the large amounts of data stored for sequence reads which are aligned against a reference genome sequence		Visualisation
Barcode generator	Generator of sequence barcodes suitable for Illumina sequencing.		DNA barcoding
Barcrawl Bartab	Barcrawl facilitates the design of barcoded primers, for multiplexed high-throughput sequencing.		DNA barcoding
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	Bill Langdon Petr Klus Simon Lam Giles Yeo Brian Lam
Batman	Bayesian tool for methylation analysis (Batman) for analyzing methylated DNA immunoprecipitation (MeDIP) profiles	DNA methylation
BayesCall	Bayesian basecaller	Sequencing	Base-calling
BayesPeak	A Bayesian hidden Markov model to detect enriched locations in ChIP-seq data.	ChIP-seq Simulation experiment	Statistical calculation
BaySeq	Identify differential expressed genes	RNA-Seq quantification	Differential expression analysis	Thomas J. Hardcastle
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	Brian Bushnell
BBSeq	Tool for analyzing RNA-Seq data to analyze gene expression	RNA-Seq quantification
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	Brad Chapman et al.
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	Aaron Quinlan
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	Sonnhammer ELL; Hollich V
BFAST	Blat-like Fast Accurate Search Tool.	Whole genome resequencing	Read mapping Sequence alignment Genome indexing	Nils Homer Stanley F. Nelson and Barry Merriman
BFCounter	BFCounter is a program for counting k-mers in DNA sequence data.		K-mer counting	Pall Melsted
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	Abuin JM Pichel JC Pena TF Amigo J
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
Bionimbus	Cloud environment for analysis of microarray and second generation sequencing data.
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
BioPerl	"BioPerl, a community effort to produce Perl code which is useful in biology. "	Genomics
BioPHP	biology tools for php.	Genomics
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	Martin A. Hansen
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	Biopython Project
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
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	BioSmalltalk Project
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
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
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	Liu Y (dnaase)
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	Felix Krueger
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	Devon P. Ryan
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
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	Nabil-Fareed Alikhan Nicola K Petty Nouri L Ben Zakour and Scott A Beatson
BLAT	Fast, accurate spliced alignment of DNA sequences		Read mapping Sequence alignment	Jim Kent
Blixem	a graphical blast viewer	Sequence analysis Phylogenetics	Sequence alignment visualisation	Sonnhammer ELL Durbin R
BOAT	Can accurately and efficiently map sequencing reads back to the reference genome.		Read mapping
Bort	Bort parses Blast output and quantifies hits by contig and read counts.	RNA-Seq quantification		Benjamin Rieger Steffen Rapp Hanno Schmidt
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)	Ben Langmead Cole Trapnell Mihai Pop Steven Salzberg
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
BRCA-diagnostic	Computational screening test for BRCA1/2 mutants in human genomic DNA	Personalised medicine
BreakDancer	BreakDancer is an application for detecting structural rearrangements and indels in short read sequencing data	Genomics Indel detection Structural variation
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	Sun R
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	Clark MJ
BS Seeker	Mapping tool for bisulfite treated reads	Epigenomics	Bisulfite mapping	Chen PY Cokus SJ Pellegrini M
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	Yuanxin Xi
BSSim	BSSim: Bisulfite sequencing simulator for next-generation sequencing.	DNA methylation Sequencing Epigenetics	Modelling and simulation	Luke You Jinyu Wu
Btrim	Btrim is a fast and lightweight software to trim adapters and low quality regions in reads.		Sequence trimming
BWA	Fast, accurate, memory-efficient aligner for short and long sequencing reads	Mapping	Read mapping	Heng Li and Richard Durbin
BWA-SW	Fast, accurate, memory-efficient aligner for long sequencing reads	Mapping	Read mapping	Heng Li and Richard Durbin
CABOG	Celera Assembler is scientific software for DNA research.	Sequence assembly (de novo assembly)	Sequence assembly
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	Ram Vinay Pandey Viola Nolte and Christian Schlötterer
CARPET	A web‐based package for the analysis of ChIP‐chip and expression tiling data	ChIP-on-chip	Genotyping
CASHX	Parse, map, quantify and manage large quantities of short-read sequence data.	Transcriptomics	Read mapping	James Carrington
CATCH	A tool for exploring patterns in ChIP profiling data.	ChIP-seq ChIP-on-chip	Sequence alignment Clustering	Nielsen FG
CatchAll	Estimate ecological diversity with both parametric and non-parametric estimators.	Metagenomics Population genetics		John Bunge
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		Piazza Rocco
CexoR	Strand specific peak-pair calling in ChIP-exo data	ChIP-exo	Peak calling	Pedro Madrigal
CGA Tools	Tools for viewing, manipulating and converting data from Complete Genomics		File reformatting
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	Jonathan Cairns Paula Freire Pritchett Mikhail Spivakov
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	Giovanna Ambrosini Philipp Bucher
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	Kulakovskiy IV Boeva VA Favorov AV Makeev VJ
CHiPSeq	From Science Johnson, 2007	ChIP-seq	Peak calling	Johnson DS Mortazavi A Myers RM Wold B
ChIPseqR	ChIP-seq qanalysis tool	ChIP-seq
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	Kallio A Hupponen T Gentile M Tuimala J Klemelä P Scheinin I Mattila K Saren A-M Naktinis R Korpelainen E
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
ChromHMM	ChromHMM is software for learning and characterizing chromatin states.	Epigenomics	Statistical calculation	Ernst J Kellis M
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	Martin I Krzywinski Jacqueline E Schein Inanc Birol Joseph Connors Randy Gascoyne Doug Horsman Steven J Jones and Marco A Marra
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
Cistrome	Galaxy-based web service for analysis of ChIP data	ChIP-seq ChIP-on-chip
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	Knudsen T Knudsen B
Clean reads	clean_reads cleans NGS (Sanger, 454, Illumina and solid) reads.		Sequencing quality control Sequence trimming
CleaveLand	A pipeline for using degradome data to find cleaved small RNA targets.	Regulatory RNA
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		Tobias Marschall
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
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	Schatz MC
ClustDB	A powerful tool for exact sequence matching
Cluster Flow	A command-line pipeline tool which uses common cluster managers to run bioinformatics analysis pipelines.		Analysis pipeline	Ewels PA
CNANorm	A normalization method for Copy Number Aberration in cancer samples.	Genomics Copy number estimation Cancer biology	Peak calling Standardisation and normalisation	Stefano Berri and Arief Gusnanto
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
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		Jose R Valverde
CnD	Program to detect copy number variation in inbred mouse strains	Copy number estimation
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
CnvHMM	WashU copy number variant (CNV) detection algorithm for Illumina/Solexa data.	Structural variation		Ken Chen Xiaoqi Shi
CNVkit	CNVkit is a software toolkit to infer and visualize copy number from targeted DNA sequencing data.	Structural variation Copy number estimation	Variant calling	Talevich E
CNVnator	CNV discovery and genotyping from read-depth analysis of personal genome sequencing	Genotyping Copy number estimation		Abyzov A Urban AE Snyder M Gerstein M
CNVseq	CNV-seq, a method to detect copy number variation using high-throughput sequencing. pubmed	Copy number estimation
CompreheNGSive	compreheNGSive is an interactive visualization of the end results of the next-generation sequencing pipeline.	Next Generation Sequencing	Visualisation	Alex Bigelow
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
ConDeTri	ConDeTri is a content dependent read trimming software for Illumina/Solexa sequencing data	Genomics RNA-Seq Sequencing	Sequence trimming
ContEst	GATK tool to estimate amount of cross-individual contaminating sequence in a dataset	Metagenomic sequencing	Sequencing quality control
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		Jason Li
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
Coral	Corrects sequencing errors in short read data via multiple alignments		Sequence error correction	L. Salmela
CORAL (Contig Ordering Algorithm)	An algorithm has been developed to order fingerprinted clones within contigs.		Sequence error correction	Teague K
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	Mario Caccamo Zamin Iqbal
CPTRA	Integrated transcriptome analysis from Sanger, 454, Solexa, SOLiD, etc reads	RNA-Seq alignment RNA-Seq quantification
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)	Philippe N Salson M Commes T Rivals E
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
CRISP	Identifies rare and common variants in pooled sequencing data	SNP detection
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
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	Cole Trapnell
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	L. Goff C. Trapnell
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)	Haimel M
Cutadapt	remove adapter sequences from high-throughput sequencing data using alignment			Marcel Martin
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	Tao Wang
DecGPU	Parallel and distributed error correction algorithm for high-throughput short reads.	Sequence assembly (de novo assembly)	Sequence error correction
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	Robert Schmieder
DeepTools	User-friendly tools for the normalization and visualization of deep-sequencing data.	Genomics ChIP-seq	Visualisation Conversion Standardisation and normalisation	Fidel Ramírez Friederike Dündar Björn Grüning Sarah Diehl Thomas Manke
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	Likun Wang Zhixing Feng Xi Wang Xiaowo Wang and Xuegong Zhang
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	Anders S
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
DiBayes	Bayesian identification of SNPs in color space (SOLiD) data	SNP detection		ABI
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	Rory Stark
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	Li SHEN
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	Raluca Uricaru Pierre Peterlongo Claire Lemaitre Rayan Chikhi Guillaume Rizk
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	Heracle BioSoft SRL
DNA Chromatogram Explorer	DNA Chromatogram Explorer is a Windows Explorer clone dedicated to DNA sequence analysis and manipulation.	Sequence analysis	File reformatting Chromatogram visualisation
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	Homer N
DNaseR	DNase I footprinting analysis of DNase-seq data in R	DNase-seq	Peak calling Nucleic acid sequence feature detection	Pedro Madrigal
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
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
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	Xi Wang
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
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
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...	Lerdrup M Johansen JV Agrawal-Singh S Hansen KH
Easyfig	Genome comparison figure generator	Comparative genomics	Comparative genomics	Mitchell J Sullivan
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
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	Robinson MD Smyth GK McCarthy DJ
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
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
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
ERANGE	ERANGE is a Python package for doing RNA-seq and ChIP-seq.	ChIP-seq RNA-Seq alignment RNA-Seq quantification DNA transcription
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
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	Prezza N Del Fabbro C Vezzi F De Paoli M Policriti A
Error Correction Evaluation Toolkit	Evaluation of error correction results	Data handling	Sequencing quality control
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
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)
ExomeCNV	Identifies copy number variation from targeted exome sequencing data	Exome capture Copy number estimation
ExomeCopy	CNV detection from exome sequencing read depth	Copy number estimation Exome and whole genome variant detection Exome analysis		Love MI
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	Ewan Birney Guy St C Slater
FAAST	Flowspace Assisted Alignment Search Tool		Read mapping
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		Henrik Stranneheim
Falcon	FALCON: experimental PacBio diploid assembler	Sequence assembly	Sequence assembly	J. Chin
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	Travis J. Lawrence Dana L. Carper Katherine C.H. Amrine Kyle Kauffman Claudia Canales and David H. Ardell
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	Simon Andrews
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	Andrews SR
FastQValidator	Checking that FastQ files are follows standards	Quality control	Sequencing quality control
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	Wei Shi and Yang Liao
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	Karen C. Dannemiller Darryl Reeves Kyle Bibby Naomichi Yamamoto Jordan Peccia
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	White JR Roberts M Yorke JA Pop M
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	Stocks MB Mapleson D Moxon S
FindPeaks 3.1	Findpeaks was developed to perform analysis of ChIP-seq experiments.	ChIP-seq	Peak calling	Anthony Fejes
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	Anthony Fejes
FLASH	Identifies paired-end reads which overlap in the middle, converting them to single long reads		Sequence assembly Read pre-processing
Flexbar	Flexible barcode and adapter processing for next-generation sequencing platforms	Genomics	Adapter removal Sequence trimming DNA barcoding Quality control Read pre-processing
Flower	Tool for reformatting SFF files into other formats or tab-delimited
FlowSim	Tool for simulating errors in 454 sequencing data		Sequence error correction Modelling and simulation
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
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		Erik Garrison
FREEC	A tool for control-free copy number alteration (CNA) detection using deep-sequencing data, particularly useful for cancer studies.	Copy number estimation
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		Piazza R
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	Daniel N
FusionHunter	Identifies gene fusions in RNA-Seq data	RNA-Seq		Li Y Ma J
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	Ge H Liu K Juan T Fang F Newman M Hoeck W
FusionSeq	Identifies fusion transcripts from paired end RNA-Seq data.	RNA-Seq Gene structure	Sequence alignment analysis	Andrea Sboner Lukas Habegger
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
G-SQZ	Huffman coding-based sequencing-reads specific representation scheme that compresses data without altering the relative order.		File reformatting
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
Galign	Identifies polymorphisms between sequence reads obtained using Illumina/Solexa technology and a reference genome	SNP detection	Read mapping
Gambit	A cross-platform GUI for sequence visualization and analysis.		Visualisation
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	Sana ME Volinia S
GASSST	Fast and accurate aligner for short an long reads		Sequence alignment Mapping	Guillaume Rizk and Dominique Lavenier
GASV	Software for classification and comparison of structural variants measured via paired-end sequencing and/or array-CGH.	Structural variation
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	Broad Institute
GBrowse	Genome Viewer		Visualisation
GeeFu	Database tool for genomic assembly and feature data	Genomics	Sequence assembly
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	Yuchun Guo Shaun Mahony & David K Gifford
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
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
GENE-Counter	GENE-counter is a computational pipeline for analyzing RNA-Sequencing (RNA-Seq) data for differential gene expression	RNA-Seq		Jason Cumbie
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	Genedata AG
... further results