Semantic search
| Name | Summary | Bio Tags | Meth Tags | Features | Language | Licence | OS |
|---|---|---|---|---|---|---|---|
| Reconciliator | The tool for merging assemblies | Sequence assembly | Perl | Linux | |||
| RECOUNT | Probabilistic tag count error correction for next generation sequencing data (Solexa/Illumina). | RNA-Seq quantification | Expectation Maximisation | C++ | GPL | Linux | |
| RefCov | WashU Reference Coverage tool for analyzing the depth, breadth, and topology of sequencing coverage | Copy number estimation | |||||
| Repitools | Toolbox of procedures to interrogate and visualize epigenomic data. Part of BioConductor | ChIP-seq ChIP-on-chip | Visualisation Sequencing quality control Statistical calculation Methylation calling | R | LGPL | ||
| Reptile | A new algorithm for short read error correction that harvests information from k-spectrum and read decomposition | Genomics | Sequencing quality control | C++ | GPL Boost | ||
| ReSeqSim | A simulation toolbox that will help us optimize the combination of different technologies to perform comparative genome re-sequencing, especially in reconstructing large structural variants (SVs). | Structural variation | Read mapping Simulation | ||||
| RGA | Reference-guided assembler | SNP detection | Sequence assembly | ||||
| RiboPicker | riboPicker is a publicly available tool that is able to automatically identify and efficiently remove rRNA-like sequences from metatranscriptomic and metagenomic datasets. riboPicker is available as both standalone and web-based versions. | Genomics Transcriptomics Metagenomics | Read pre-processing RRNA filtering | Perl C | GPLv3 | UNIX Mac OS X | |
| RMAP | Assembles 20 - 64 bp Solexa reads to a FASTA reference genome. By Andrew D. Smith and Zhenyu Xuan at CSHL. (published in BMC Bioinformatics). POSIX OS required. | DNA methylation | Read mapping Bisulfite mapping | GPLv3 | Linux Mac OS X | ||
| RNA | A randomized Numerical Aligner for Accurate alignment of NGS reads | Mapping | Read mapping | Fast Accurate | C++ | GPLv3 | Linux UNIX Windows Mac OS X |
| RNA-MATE | A recursive mapping strategy for high-throughput RNA-sequencing data. | RNA-Seq alignment RNA-Seq quantification | |||||
| RNASEQR | a streamlined and accurate RNA-seq sequence analysis program | Alternative splicing | Read mapping | ||||
| Rnnotator | Automated software pipeline that generates transcript models by de novo assembly of RNA-Seq data without the need for a reference genome | Sequence assembly (de-novo assembly) Transcriptome assembly | Commercial Freeware | ||||
| RobiNA | RobiNA is a Java GUI that enables the user to graphically call differentially expressed genes. For read mapping it relies on bowtie and for the differntial expression analysis it builds on an R backbone running DESeq and edgeR. | RNA-Seq | Differential expression analysis | Sequence trimming differential expression graphical display | Java R | GPL | Windows Linux Mac OS X |
| Rolexa | Allows fast and accurate base calling of Solexa's fluorescence intensity files and the production of informative diagnostic plots. | Sequencing | Base-calling | R | |||
| RSAT peak-motifs | A workflow combining a series of time- and memory-efficient motif analysis tools to extract motifs from full-size collections of peaks as generated by ChIP-seq, ChIP-chip or other ChIP-X technologies. | ChIP-seq Epigenomics Gene regulation | Sequence motif recognition Sequence motif comparison Sequence motif discovery | Perl CGI Python C | Commercial Freeware | UNIX Mac OS X Linux | |
| RSEM | We present a generative statistical model and associated inference methods that handle read mapping uncertainty in a principled manner. Through simulations parameterized by real RNASeq data, we show that our method is more accurate than previous methods. Our improved accuracy is the result of handling read mapping uncertainty with a statistical model and the estimation of gene expression levels as the sum of isoform expression levels. | RNA-Seq alignment RNA-Seq quantification | C++ | ||||
| RSEQtools | RSEQtools includes a format specification for RNA-Seq data that provides confidentially-aware; data summaries as well as several tools for performing common analyses: expression measurements (e.g. RPKMs), creation of signal tracks, segmentation, annotation manipulations, etc. | RNA-Seq quantification | C | Creative Commons - Attribution; Non-commercial 2.5 | Mac OS X UNIX Linux | ||
| Rsolid | Rsolid implements a version of the quantile normalization algorithm that transforms the intensity values before calling colors | Base-calling | R C | ||||
| Rsubread | Rsubread is Bioconductor R package, which provides facilities to performing read alignments using the Subread aligner. It also includes other functionalities such as featureCounts read summarisation function. | Next Generation Sequencing | Read mapping Read summarisation Quality assessement | R C | GPLv3 | Linux 64 Mac OS X; x86 64 Mac OS X | |
| RTG | Comprehensive analysis pipelines powered with unique mapping speed and sensitivity deliver deep genomic analysis in variant detection and metagenomic applications with Illumina, Ion Torrent, Complete Genomics and Roche 454 data sets. | SNP detection Indel detection Metagenomics Exome and whole genome variant detection | Read mapping Sequence alignment K-mer counting Sequence contamination filtering Read depth analysis Translated nucleotide search Species frequency estimation | Commercial free for non-commercial academic research | Linux Mac OS X Windows | ||
| RUbioSeq | RUbioSeq has been developed to facilitate the primary and secondary analysis of resequencing projects by providing an integrated software suite of parallelized pipelines to detect exome variants (SNVs and CNVs) and to perform Bisulfite-seq analyses automatically. RUbioSeq's variant analysis results have been already validated and published. AVAILABILITY: http://rubioseq.sourceforge.net/ | DNA methylation Sequencing Copy number estimation Epigenetics Exome analysis | Variant calling | Perl | UNIX | ||
| S-MART | S-MART manages your RNA-Seq and ChIP-seq data. | ChIP-seq RNA-Seq | Python Java | Linux Mac OS X Windows | |||
| SAMMate | GUI for processing SAM/BAM and BED files. The software allows users to accurately estimate gene expression scores using short reads originating from both exons and exon-exon junctions, to generate wiggle files for visualization in UCSC genome browser, and to generate an alignment statistics report. | RNA-Seq quantification | Sequence analysis | Java | GPLv3 | Windows Mac OS X | |
| Samscope | Samscope is a lightweight SAM/BAM file viewer that makes visually exploring next generation sequencing data as intuitive as Google Maps. Samscope uses multiple layers to simultaneously (or sequentially) view SAM/BAM related features like coverage or allele frequency, or ChIP-SEQ features like polarity from as many files as you like. The paging-friendly binary file layout makes it feasible to browse data sets far larger than the system's available RAM. | Genomics ChIP-seq RNA-Seq | Read mapping Visualisation | C++ | AGPL | POSIX Linux | |
| SAMStat | SAMStat is an efficient C program for displaying statistics of large sequence files. | Sequencing quality control | C | GPLv3 | UNIX | ||
| SAMtools | Various utilities for processing alignments in the SAM format, including variant calling and alignment viewing. | SNP detection | Sequence assembly visualisation Modelling and simulation | Integrated solution API | C | MIT | |
| Savant Genome Browser | Savant is a genome browser which combines visualization of HTS and other genome-based data with powerful analytic tools. | Genomics | Visualisation Sequence alignment visualisation | Plugin framework Bookmarking Table View fast memory efficient | Java | Apache License 2.0 | Windows Linux all supporting JVM Mac OS X |
| Scaffolder | Edit your genome sequence using a simple human readable syntax. Manage contig positions and add inserts all in a plain text file. | Scaffolding | Ruby | MIT | Linux Mac OS X | ||
| ScaffViz | Introduction The AMOSViewer is a plugin for Cytoscape. It displays scaffold assembly graphs generated by a scaffolder. | Sequence assembly | Sequence assembly | ||||
| SCALCE | SCALCE (skeɪlz) is fast FASTQ compression utility that utilizes locally consistent parsing for better compression rate. It achieves around 2X more compression than gzip alone. | Genomics | File reformatting | FASTQ file compression | C | Linux 64 Linux | |
| SCARF | Scaffolded and Corrected Assembly of Roche 454 (SCARF) is a next-generation sequence assembly tool for evolutionary genomics that is designed especially for assembling 454 EST sequences against high-quality reference sequences from related species. | Sequence assembly | GPLv3 | ||||
| Scripture | Tool for assembling transcriptome from paired-end Illumina RNA-Seq data | RNA-Seq alignment | |||||
| SEAL | Read mapper and duplicate remover. | Read mapping | Python C++ Java | GPLv3 | |||
| SEECER | Sequence error correction for RNA-Seq data | RNA-Seq quantification | Sequence error correction | supports multicore processors | C | ||
| SEED | Tool to cluster sequence reads prior to assembly or other operations. | Metagenomics | Sequence clustering | C++ | Mac OS X Linux Windows | ||
| Segemehl | Map short reads to known genome with tolerance for mismatches and indels using suffix arrays for high accuracy matching | Genomics | Mapping | fast precise low cost for high-error matching | C C++ | ||
| Segtor | A software tool to annotate large sets of genomic coordinates, intervals, SNVs, indels and translocations with respect to known genes. | SNP | Annotation SNP annotation | SNP annotation | Perl C | Non-commercial | Linux Mac OS X |
| Seq2HLA | seq2HLA is a computational tool to determine Human Leukocyte Antigen (HLA) directly from existing and future short RNA-Seq reads. It takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising known HLA alleles and outputs the most likely HLA class I and class II types, a p-value for each call, and the expression of each class. | Transcriptomics Mapping | Read mapping Genetic variation analysis | Python R | Unix Mac OS X | ||
| SeqAn | C++ template library with many sequence analysis algorithms and datastructures. | Genomics Sequence analysis Phylogenetics | C++ | BSD (3-clause) | UNIX Mac OS X Windows | ||
| SeqBuster | SeqBuster, a web-based bioinformatic tool offering a custom analysis of deep sequencing data at different levels, with special emphasis on the analysis of miRNA variants or isomiRs and the discovering of new small RNAs. | Transcriptomics Regulatory RNA | Read mapping Annotation | Annotation and detection of miRNAs and other small RNAs | Java R | Commercial Freeware | Mac OS X Linux |
| SeqCons | SeqCons is an open source consensus computation program for Linux and Windows. The algorithm can be used for de novo and reference-guided sequence assembly. | Sequence assembly | Linux Windows | ||||
| SeqEM | Genotype-calling algorithm that estimates parameters underlying the posterior probabilities in an adaptive way rather than arbitrarily specifying them a priori. The algorithm applies the well-known EM algorithm to an appropriate likelihood for a sample of unrelated individuals with next-generation sequence data, leveraging information from the sample to estimate genotype probabilities and the nucleotide-read error rate. | SNP detection | Expectation Maximisation | ||||
| SeqGSEA | Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing | Genomics RNA-Seq Biomedical Sciences | Statistical calculation Functional enrichment Functional analysis | integrative analysis | R | GPL (>= 3) | any |
| SeqMan NGen | Sequence assembly software using traditional and next-gen techonologies. Subsequent analysis of the assembly, including variant discovery, coverage evaluation and consensus annotation is provided through full integration with Lasergene. | Sequence assembly (de-novo assembly) Sequence assembly (de novo assembly) Whole genome resequencing Genomics ChIP-seq RNA-Seq alignment SNP detection Indel detection Transcriptome assembly | Sequence assembly Read mapping Sequence alignment | Commercial | Windows 7 64-bit or Higher Mac OS X 10.7 10.8 or 10.9 Linux Ubuntu 12.04 Linux CentOS 6.5 | ||
| SeqMap | SeqMap is a tool for mapping large amount of short sequences to the genome. | Read mapping | command line parallel execution | Mac OS X Windows Linux | |||
| SeqMINER | seqMINER is an integrated portable ChIP-seq data interpretation platform with optimized performances for efficient handling of multiple genomewide datasets. seqMINER allows comparison and integration of multiple ChIP-seq datasets and extraction of qualitative as well as quantitative information. seqMINER can handle the biological complexity of most experimental situations and proposes supervised methods to the user in data categorization according to the analysed features. In addition, through multiple graphical representations, seqMINER allows visualisation and modelling of general as well as specific patterns in a given dataset. Moreover, seqMINER proposes a module to quantitatively analyse correlations and differences between datasets. | ChIP-seq | Java | GPLv3 | platform-independent | ||
| SeqMonk | A tool to visualise and analyse high throughput mapped sequence data | Genomics Epigenomics | Visualisation Sequence assembly visualisation Sequence alignment visualisation Statistical calculation | Genome Viewer Data Visualisation Data Quantitation filtering and analysis | Java | GPLv3 | Windows Mac OS X Linux |
| SeqPrep | Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. | Sequence assembly (de novo assembly) Genomics | Merges overlapping paired-end reads strips adapters off of reads. | C | MIT | POSIX | |
| SeqSaw | A package for mapping of spliced reads and unbiased detection of novel splice junctions from RNA-seq data. | RNA-Seq Alternative splicing | Read mapping Sequence alignment | Short Spliced Sequence Mapping Tool | C++ | GPL | Linux |
| SeqSeg | An algorithm to identify chromosomal breakpoints using massively parallel sequence data | Copy number estimation | Matlab | ||||
| SeqSite | SeqSite is an efficient and easy-to-use software tool implementing a novel method for identifying and pinpointing transcription factor binding sites. It first detects transcription factor binding regions by clustering tags and statistical hypothesis testing, and locates every binding site in detected binding regions by modeling the tag profiles. It can pinpoint closely spaced adjacent binding sites from ChIP-seq data. This software is coded in C/C++, and supports major computer platforms. | ChIP-seq | Peak calling | stand-along software tool can run on major computer platforms | C C++ | GPL | Linux Mac OS X Windows |
| SeqSolve | Simple analysis of Next Generation Sequencing data. | Transcriptomics ChIP-seq RNA-Seq Alternative splicing | Ab-initio gene prediction Differential expression analysis Quality control | User-friendly Scientifically relevant Reliable Scalable | Commercial | Windows Linux | |
| SeqSphere+ | Ridom SeqSphere+ Software is designed for distributed work-groups (client/server model) and allows automatic processing, assembling and analyzing of NGS (e.g., Illumina, Ion Torrent or PacBio) and Sanger capillary-electrophoresis sequence data. SeqSphere+ is the solution for easy and automated microbial analysis; enabling your lab to employ whole genome microbial typing (cgMLST or MLST+), traditional MLST or eMLST/rMLST sequencing projects. | Comparative genomics Microbial Surveillance | Sequence assembly Read mapping Variant calling | Advanced and user-friendly analyses of genomic microbial NGS and Sanger data | Java | Commercial | Windows Linux 64 |
| SeqTrim | A pipeline for preprocessing sequences. | Sequence trimming | |||||
| Sequedex | Sequedex classifies short reads for phylogeny and function at high speed | Genomics Metagenomics Phylogenetics | Sequence analysis Sequence annotation | Fast protein fragments identified | Java Python | Commercial Freeware | Linux 64 Mac OS X |
| SequenceVariantAnalyzer | DNA sequence information underpins genetic research, enabling discoversies of important biological or medical benefit. Compared with previous discovery strategies, a whole-genome sequencing study is no longer constrained by differing patterns of linkage disequilibrium, thus, in theory, is more possible to directly identify the gentic variants contributing to biological traits or medical outcomes. The rapidly evolving high-throughput DNA sequencing technologies have now allowed the fast generation of large amount of sequence data for the purpose of performing such whole-genome sequencing studies, at a reasonable cost. SequenceVariantAnalyzer, or SVA, is a software tool that we have been developing to analyze the genetic variants identified from such studies. URL: http://www.svaproject.org/ | Genomics Personalised medicine Sequence analysis Genetic variation | Annotation SNP calling Genome visualisation | Variant annotation and analysis | Java | Linux 64 | |
| Sequencher | Desktop alignment software now with plugins to MAQ and GSNAP for NGS sequence date | Sequence assembly (de novo assembly) SNP detection | Sequence assembly Sequence alignment | Bisulfite sequencing consensus sequence generation and export SNP/InDel/Read Error display and search | Commercial | Windows Mac OS X | |
| SeqWare | SeqWare provides tools designed to support massively parallel sequencing technologies. | Laboratory information management Workflows | Java | GPLv3 | Linux | ||
| SeqWords | SeqWords is a featherweight object for the calculation of n-mer word occurrences in a single sequence. | K-mer counting | Part of BioPerl | Perl | Perl artistic licence | ||
| SESAME | Gnotyping of multiplexed individuals for several markers based on NGS amplicon sequencing. | Exome capture Genotyping | GPLv3 | Windows Linux | |||
| SEWAL | Processing of deep sequencing data from in vitro selection experiments | In vitro selection | |||||
| Sff2fastq | The program 'sff2fastq' extracts read information from a SFF file, produced by the 454 genome sequencer, and outputs the sequences and quality scores in a FASTQ format. | Conversion | Linux | ||||
| SGA | SGA is a de novo assembler designed to assemble large genomes from high coverage short read data. | Sequence assembly | C++ | GPLv3 | Linux | ||
| SHARCGS | SHARCGS is a suitable tool for fully exploiting novel sequencing technologies by assembling sequence contigs de novo with high confidence and by outperforming existing assembly algorithms in terms of speed and accuracy. | Sequence assembly (de novo assembly) | Sequence assembly | Perl | Linux | ||
| SHE-RA | The SHE-RA software turns error-prone short reads into Sanger-quality composite reads. | Sequence error correction | Open Source | ||||
| Sherman | bisulfite-treated Read FastQ Simulator | Genomics DNA methylation Sequencing Epigenetics | Modelling and simulation | Perl | GPLv3 | Linux Mac OS X | |
| ShoRAH | Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes. | Metagenomics | Read mapping Haplotype inference | GPLv3 | Linux Mac OS X | ||
| Shore | Analysis suite for short read data. | SNP detection Structural variation | Mapping | Linux Mac OS X POSIX | |||
| SHOREmap | Extension of the short read analysis pipeline SHORE. SHOREmap supports genome-wide genotyping and candidate-gene sequencing in a single step through analysis of deep sequencing data from a large pool of recombinants. | Perl R | GPLv3 | ||||
| ShortFuse | Method for using paired-end reads to find fusion transcripts without requiring unique mappings or additional single read sequencing | C++ Python | |||||
| ShortRead | ShortRead is an R/BioConductor package for input, quality assessment, manipulation, and output of high-throughput sequencing data. | R | |||||
| SHORTY | SHORTY is targetted for de novo assembly of microreads with mate pair information and sequencing errors. SHORTY has some novel approach and features in addressing the short read assembly problem.. | Sequence assembly (de novo assembly) | Sequence assembly | C++ Perl | |||
| SHRAP | A sequencing protocol and assembly methodology that utilizes high-throughput short-read technologies. | Sequence assembly (de novo assembly) | Sequence assembly | ||||
| SHREC | A new algorithm for correcting errors in short-read data that uses a generalized suffix trie on the read data as the underlying data structure | Sequencing quality control Sequence error correction | Java | ||||
| SHRiMP | Assembles to a reference sequence. Developed with Applied Biosystem's colourspace genomic representation in mind. Authors are Michael Brudno and Stephen Rumble at the University of Toronto. Works with data in letterspace (Roche, Illumina), colourspace (AB) and Helicos space. | Read mapping | colourspace | ||||
| Sibelia | Sibelia: A comparative genomic tool: It assists biologists in analysing the genomic variations that correlate with pathogens, or the genomic changes that help microorganisms adapt in different environments. Sibelia will also be helpful for the evolutionary and genome rearrangement studies for multiple strains of microorganisms. | Genomics | Variant calling | C++ | GPL | ||
| SICER | A clustering approach for identification of enriched domains from histone modification ChIP-seq data. | ChIP-seq Epigenomics | Sequence contamination filtering | Python | |||
| SiLoCo | Compares sRNA expression levels in multiple samples by grouping sRNAs into loci based on genomic location | Workflows | Gene expression profiling | Java | Custom Licence | Linux 64 Windows Mac OS X | |
| Sim4cc | Cross-species spliced alignment of ESTs to genomes | RNA-Seq alignment Comparative genomics | Read mapping | C++ | GPLv2 | UNIX Linux | |
| SimNext | Sequencing read simulator | Modelling and simulation | Perl | ||||
| SimSeq | Illumina paired-end and mate-pair short read simulator. Used to sample reads from the simulated genome for the first Assemblathon. | Genomics | Modelling and simulation | Position and underlying base specific error model. Simulates chimeric mate-pair reads with paired-end contamination and duplicates. | Java C | MIT | POSIX |
| Sissrs | Produce a list of peakmaxima from aligned positions. | ChIP-seq | Peak calling | Perl | Linux UNIX | ||
| Skewer | Skewer implements a novel dynamic programming algorithm dedicated to the task of adapter trimming and it is specially designed for processing illumina paired-end sequences. | Sequence assembly RNA-Seq Small RNA Sequencing | Read mapping Adapter removal Sequence trimming Read pre-processing | multi-threading | C++ | Linux 64 | |
| Slider | A new alignment approach that reduces the alignment problem space by utilizing each read base's probabilities given in the Illumina prb files. | SNP detection | Mapping | Java | |||
| SlideSort | SlideSort finds all similar pairs from a string pool in terms of edit distance. Using an efficient pattern growth algorithm, SlideSort discovers chains of common k-mers to narrow down the search. | Clustering | C++ | Linux Windows | |||
| SLOPE | Detects structural variants from targeted short DNA reads | Exome capture Structural variation | C++ | ||||
| SmashCommunity | SmashCommunity is a stand-alone metagenomic annotation and analysis pipeline suitable for data from Sanger and 454 sequencing technologies. | Metagenomics | |||||
| SNIP-Seq | Tool for discovering SNPs in population sequencing data | SNP detection | Python | ||||
| Sniper | SNP detection utilizing multi-mapping reads | SNP detection | C Python | UNIX Mac OS X | |||
| SNP-o-matic | SNP-o-matic is a fast, memory-efficient and stringent read mapping tool offering a variety of analytical output functions, with an emphasis on genotyping. | SNP detection | Read mapping | C++ C | |||
| SNPsea | SNPsea is an algorithm to identify cell types and pathways likely to be affected by risk loci. | SNP detection Functional genomics Gene expression analysis | Enrichment | C++ R Python | GPLv3 |
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| SNPSeeker | Identification of SNPs in pooled genomic samples | SNP detection | C | ||||
| SNVer | Variant calling in pooled or individual sequence data. | SNP detection | Java | Windows Linux Mac OS X | |||
| SNVMix | Detects single nucleotide variants from next generation sequencing data. | SNP detection | C | MIT | |||
| SOAP | SOAP (Short Oligonucleotide Alignment Program) is a program for efficient gapped and ungapped alignment of short oligonucleotides onto reference sequences. SOAP2 is an updated program based on Burrows-Wheeler Transform. | SNP detection | Read mapping Sequence alignment Genome indexing (Burrows-Wheeler) | C++ | UNIX | ||
| SOAPdenovo | SOAPdenovo, a short read de novo assembly tool, is a package for assembling short oligonucleotide into contigs and scaffolds. | Sequence assembly (de novo assembly) | Sequence assembly | Has a modular structure and comes with a read corrector an assembly module a scaffolder and a gap filler | GPLv3 | Linux Mac OS X | |
| SOAPfusion | SOAPfusion is a novel tool for fusion discovery with paired-end RNA-Seq reads. The tool follows a different strategy by “finding fusions directly and verifying them”, differentiating it from all other existing tools by “finding the candidate regions and searching for the fusions afterwards”. This enables the fusion discovery process to be more effective and sensitive, also with a specular performance under low coverage of sequencing far more better than other tools. http://soap.genomics.org.cn/SOAPfusion.html | Transcriptomics RNA-Seq Gene structure | finding fusions directly and verifying them | Perl C++ | Linux 64 | ||
| SOAPsnp | SOAPsnp is an accurate consensus sequence builder based on soap1 and SOAPaligner/soap2's alignment output. It calculates a quality score for each consensus base, which can be used for any latter process to call SNPs. | SNP detection | C C++ | ||||
| SOCS | SOLiD reference based, un-gapped alignment with bisulfite capability | DNA methylation RNA-Seq alignment SNP detection | Read mapping Bisulfite mapping | coverage colourspace Bisulfite sequencing | C++ | GPLv3 | POSIX |
| Solas | Given gene annotation the major questions addressed by the package are: prediction of alternative exons in a single condition / cell sample, prediction of differential alternative exons between two conditions / cell samples, quantification of alternative splice forms in a single condition / cell sample | RNA-Seq quantification Alternative splicing | R | ||||
| Sole-Search | Determines statistically significant peaks from ChIP experiments | ChIP-seq | Java | ||||
| SolexaQA | User-friendly software package designed to generate detailed statistics and at-a-glance graphics of sequence data quality both quickly and in an automated fashion. This package contains associated software to trim sequences dynamically using the quality scores of bases within individual reads. | Sequencing quality control Sequence trimming | Quality Processing Algorithm Runtime Speed | Perl R | GPLv3 | Mac OS X UNIX | |
| SolexaTools | SolexaTools is a project to create a tool set to work with a Solexa genome sequencer. It includes multiple components including a LIMS system, pipeline and other tools to support end-users and researchers setting up a Solexa environment. | Laboratory information management | Java | ||||
| SOLID software tools | SOLID software tools hosted by Applied Biosystems | Commercial | |||||
| SomaticCall | Finds single-base differences (substitutions) between sequence data from tumor and matched normal samples. | Genetic variation | |||||
| Spiral Genetics | Spiral Genetics provides a novel aligner/variant caller, Anchored Assembly, which can detect large structural variations using short read NGS data with unmatched precision. | Sequence assembly Whole genome resequencing SNP detection Mapping Sequence analysis Statistical calculation DNA-Seq Exome and whole genome variant detection Genomic assembly Quality control | Read mapping Sequence alignment File reformatting | Accurate Fast Cloud Computing Read mapping SNP calling command line large SV detection | C++ | Commercial | Linux Mac OS X Windows |
| SpliceGrapher | SpliceGrapher is a package for creating splice graphs from RNA-Seq data, guided by gene models and EST data (when available). | Alternative splicing | Visualisation | ||||
| SpliceMap | Detects splice junctions from RNA-seq data. This method does not depend on any existing annotation of gene structures and is capable of finding novel splice junctions with high sensitivity and specificity. It can handle long reads (50–100 nt) and can exploit paired-read information to improve mapping accuracy. | RNA-Seq alignment | Read mapping | Python C++ | Linux | ||
| SplicePlot | SplicePlot is a simple command line utility that produces intuitive visualization of alternative splicing and splicing quantitative trait loci (sQTL) and their effects | Alternative splicing | Visualisation | ||||
| SpliceTrap | SpliceTrap is a statistic tool for quantifying exon inclusion ratios in paired-end RNA-seq data. Instead of full transcript quantification, SpliceTrap approaches to exon inclusion level estimation as a Bayesian inference problem. For every exon it quantifies the extent to which it is included, skipped or subjected to size variations due to alternative 3’/5’ splice sites or Intron Retention. | RNA-Seq RNA-Seq quantification Alternative splicing | Statistical calculation | Splicing ratio estimation | C++ Perl | UNIX Linux | |
| SplicingViewer | SplicingViewer is an integrated tool developed to enable users to detect the splice junctions, annotate alternative splicing events, and visualization of the patterns of alternative splicing events. | Genomics RNA-Seq | Mapping | GUI command line Data Visualisation | Java | GPL Commercial BioLicense LGPL BSD License | Linux Windows Mac OS X |
| SPLINTER | Identification of indel variants in pooled DNA with spike-in controls | SNP detection Indel detection | finds rare indels in pooled samples error model profiler for sequencing library | C C++ | Commercial Freeware | ||
| SplitSeek | de novo prediction of splice junctions in short-read RNA-seq data, suitable for detection of novel splicing events and chimeric transcripts. | RNA-Seq alignment | Perl | GPL | |||
| SPP | R-scripts for ChIP-seq analysis. | Genomics ChIP-seq | Peak calling | multi-threading | R | ||
| SR-ASM | SR-ASM algorithm is designed for DNA assembly of the short sequences coming from 454 sequencers. | Sequence assembly (de novo assembly) | Sequence assembly | C++ | Linux UNIX | ||
| SRAdb | R tool to query Short Read Archive and download data from it | R | |||||
| SRMA | SRMA is a short read micro re-aligner for next-generation high throughput sequencing data. | SNP detection Indel detection | Localised reassembly | Java C | GPL | ||
| SSA | SSA (Signal Search Analysis) is a software package for the analysis of nucleic acid sequence motifs that are postionally correlated with a functional site (e.g a transcription or translation initiation site). | Sequence motifs | Sequence analysis Sequence motif comparison Sequence motif discovery | Fortran F77 C Perl | GPL | Linux Mac OS X | |
| SSAHA | SSAHA (Sequence Search and Alignment by Hashing Algorithm) is an algorithm for very fast matching and alignment of DNA sequences. | Sequence alignment Local sequence alignment | Commercial Freeware | Linux Mac OS X | |||
| SsahaSNP | Sequence Search and Alignment by Hashing Algorithm | SNP detection | Mac OS X Linux 64 Linux Solaris Compaq Alpha | ||||
| SSAKE | The Short Sequence Assembly by K-mer search and 3' read Extension (SSAKE) is a genomics application for aggressively assembling millions of short nucleotide sequences by progressively searching for perfect 3'-most k-mers using a DNA prefix tree. SSAKE is designed to help leverage the information from short sequences reads by stringently clustering them into contigs that can be used to characterize novel sequencing targets. Authors are René Warren, Granger Sutton, Steven Jones and Robert Holt from the Canada's Michael Smith Genome Sciences Centre. Perl/Linux. Please note that paired reads need to be in one pseuod fasta line separated by ':' >readpair:1000 ACGATAGCTTCG:ACGCGATAGATC | Sequence assembly | Perl | GPLv2 | Linux | ||
| SSPACE | Stand-alone scaffolder of pre-assembled contigs using paired-read data. | Genomics | Scaffolding | Scaffold contigs using paired reads. Extension of unmapped reads. Visualisation and tracking of contigs on scaffolds. | Perl | Windows Linux Mac OS X | |
| STADEN | Includes GAP4, GAP5, SPIN, TREV, and numerous smaller tools. | Sequence assembly Sequence alignment Visualisation | Integrated solution | C C++ Tcl Fortran | BSD | Linux Windows Mac OS X UNIX | |
| Stampy | Uses a hybrid mapping algorithm and a detailed statistical model to achieve both speed and sensitivity, particularly when reads include sequence variation. | Read mapping | Python | Commercial Freeware | Linux | ||
| Standalone hamming | Example software for decoding error-correcting barcodes | Sample Barcoding | Python | ||||
| Standardized Velvet Assembly Report | A set of scripts and a Sweave report used to iterate through parameters and generate a report on Velvet-generated sequence assemblies | Quality control | Visualisation | R Perl | GPLv3 | ||
| STAR | Ultrafast universal RNA-seq aligner | Transcriptomics RNA-Seq | Sequence alignment | C++ | GPLv3 | Linux Unix Mac OS X; x86_64 | |
| Strelka | Strelka is an analysis package designed to detect somatic SNVs and small indels from the aligned sequencing reads of matched tumor-normal samples. | Genetic variation | Variant calling | Multicore | Perl | Linux | |
| Subjunc | The Subread read aligner and Subjunc junction detector employ a novel read mapping paradigm called "seed-and-vote" to achieve a fast mapping speed and a high mapping accuracy. The seed-and-vote paradigm is particularly powerful in detecting indels. Subjunc can be used to discover exon-exon junctions from RNA-seq data. It takes Subread less than 20 minutes to map 10 million 100bp reads using one thread. Its running time remains nearly the same when mapping longer reads thanks to the high scalability of the seed-and-vote paradigm. Subread and Subjunc can be used to map reads generated from all major sequencing platforms including Illumina GA/HiSeq, Roche 454, ABI SOLiD and Ion Torrent. They can run on both Linux/unix and Mac computers. Subread and Subjunc were published in Nucleic Acids Research in 2013. | RNA-Seq alignment Mapping Sequencing RNA splicing | Read alignment | ||||
| Subread | Subread is a general-purpose read aligner which can be used to map both genomic DNA-seq reads and RNA-seq reads. It uses a new mapping paradigm called "seed-and-vote" to achieve fast, accurate and scalable read mapping. It automatically determines if a read should be globally or locally aligned, therefore particularly powerful in mapping RNA-seq reads. It supports indel detection and can map reads with both fixed and variable lengths. | Whole genome resequencing RNA-Seq alignment Mapping Next Generation Sequencing | Read mapping | Gapped alignment Local alignment Memory efficient and fast Paired read support RNAseq analysis SAM format output SNP/indel discovery in any format can run on major computer platforms capable of using very small seeds for splice mapping low cost for high-error matching paired-end mapping parallel execution short and long reads | C | GPLv3 | Linux 64 Mac OS X Mac OS X; x86 64 |
| SuccinctAssembly | Tools to build & analyze compact versions of de Bruijn graphs. | Sequence assembly (de novo assembly) | Linux | ||||
| SUDS genome browser | Compressed suffix tree implementation to browser genome sequences | Genome visualisation | C++ | GPLv2 | |||
| Suffixerator | Compute enhanced suffix array | Genome indexing (suffix arrays) | Part of GenomeTools | Linux | |||
| Supersplat | Using a genomic reference and RNA-seq high-throughput sequencing datasets, supersplat empirically identifies potential splice junctions at a rate of (~)11.4 million reads per hour. | RNA-Seq alignment | Sequence assembly | C++ | |||
| SUTTA | De novo assembly algorithm for assembling bacterial genomes from second generation sequencing data | Sequence assembly (de novo assembly) | Commercial Freeware | ||||
| SVDetect | Identifies genomic structural variations from paired-end and mate-pair next-generation sequencing data produced by the Illumina GA and ABI SOLiD platforms. Applying both sliding-window and clustering strategies, we use anomalously mapped read pairs provided by current short read aligners to localize genomic rearrangements and classify them according to their type, e.g. large insertions-deletions, inversions, duplications and balanced or unbalanced inter-chromosomal translocations | Structural variation | Perl | ||||
| SVMerge | Pipeline for the detection of structural variants by integrating calls from multiple structural variant callers. | Structural variation | Perl | ||||
| Swalign | A simple Smith-Waterman alignment implementation in C | Sequence alignment | C | MIT | |||
| SWAP454 | A program for calling SNPs using 454 read data. | SNP detection | |||||
| SwDMR | swDMR: a sliding window approach to identify differentially methylated regions based on bisulfite sequencing | DNA methylation Sequencing Epigenetics | Methylation calling | Differentially methylated regions identification and annotation | Perl R | GPLv3 | Linux UNIX |
| Swift | Primary Data Analysis for the Illumina Solexa Sequencing Platform. | Base-calling | C++ | LGPL | Linux | ||
| SWT | WashU Sliding Window Tool for detecting copy number variants from Illumina/Solexa data. | Copy number estimation | |||||
| SXOligoSearch | SXOligoSearch is a commercial platform offered by the Malaysian based Synamatix. Will align Illumina reads against a range of Refseq RNA or NCBI genome builds for a number of organisms. Web Portal. OS independent. | Sequence alignment | |||||
| Syapse | Syapse is a platform and application suite for bringing together omics and clinical data. | Genomics Transcriptomics DNA methylation ChIP-seq SNP detection Indel detection RNA-Seq Metagenomics DNA transcription Epigenomics Structural variation Population genetics Comparative genomics DNA-Seq Regulatory genomics | Visualisation Sequence analysis Differential expression analysis Ontology comparison Exome analysis Variant classification | API Cloud Computing GUI | |||
| Syzygy | Software to identify variants from pooled sequencing data | SNP detection Indel detection | Python R | ||||
| T-lex | Here, we present a computational pipeline (T-lex) that uses NGS data to detect the presence/absence of annotated Transposable Element (TE) copies. T-lex can use data from a large number of strains and returns estimates of population frequencies of individual TE insertions in a reasonable time. | Mobile genetic elements | Perl | ||||
| Ta-si prediction | ta-siRNA (trans-acting short interfering RNA): prediction of phased ta-siRNAs in plant sRNA datasets. | Workflows | Phase pattern prediction | Java | Custom Licence | Linux 64 Windows Mac OS X | |
| Tablet | Tablet is a lightweight, high-performance graphical viewer for next generation sequence assemblies and alignments. | Genomics Genotyping Comparative genomics | Sequence assembly visualisation | Sequence assembly visualisation | Java | BSD | Windows OS X Linux |
| TagCleaner | TagCleaner can be used to automatically detect and efficiently remove tag sequences (e.g. WTA or MID tags) from metagenomic datasets. TagCleaner is available as both standalone and web-based versions. | Transcriptomics Metagenomics | Sequence trimming | GPLv3 | UNIX Mac OS X Windows | ||
| TagDust | TagDust, a program identifying artifactual sequences in large sequencing runs. Given a user-defined cutoff for the false discovery rate (FDR), TagDust identifies all reads explainable by combinations and partial matches to known sequences used during library preparation. | Sequencing quality control | C | GPL | Solaris UNIX Linux | ||
| Taipan | Taipan uses greedy extensions for contig construction but at each step realizes enough of the corresponding read graph to make better decisions as to how assembly should continue. We show that this approach can achieve an assembly quality at least as good as the graph-based approaches used in the popular Edena and Velvet assembly tools using a moderate amount of computing resources. | Sequence assembly (de novo assembly) | Sequence assembly | ||||
| Tally | Tally is a program for deduplicating sequence fragments for both single and paired end input. Single reads, paired-end reads. | Sequencing | Sequence contamination filtering Read pre-processing Sequence redundancy removal | Memory efficient and fast. | C | GPLv3 | Linux UNIX Mac OS X |
| Tallymer | A collection of flexible and memory-efficient programs for k-mer counting and indexing of large sequence sets. | K-mer counting Genome indexing (suffix arrays) | Part of GenomeTools | Linux | |||
| TAPyR | Efficient BWT-based read aligner supporting multiple sequencing platforms | Whole genome resequencing | Read mapping | C | GPL | ||
| TASE | Rapid tag-counting and annotation software tool specifically designed for Illumina CASAVA sequencing datasets. | RNA-Seq quantification | Java | ||||
| TASR | Exome capture of short read data to identify the presence of variants | Exome capture | Sequence assembly | Perl | GPLv2 | ||
| TEQC | Quality assessment of target enrichment experiments. | Exome capture | Sequencing quality control | R | |||
| TileQC | TileQC: a system for tile-based quality control of Solexa data. | Sequencing quality control | R | ||||
| TiMat2 | TiMAT2 contains tools for genomic tiling microarray analysis | Genotyping | Java | BSD | |||
| TMAP | TMAP is a short read aligner specifically tuned for data from the Ion Torrent PGM | Read mapping | |||||
| TopHat | TopHat is a fast splice junction mapper for RNA-Seq reads. | RNA-Seq alignment | Sequence alignment Mapping | C++ | Boost | Linux Unix | |
| TopHat-Fusion | Detection of fusion genes in RNA-Seq data | ||||||
| TOTALRECALLER | Improves sequence quality of reads and reduces ambiguous mappings | Base-calling | Commercial Freeware | Linux | |||
| Tracembler | Tracembler streamlines the process of recursive database searches, sequence assembly, and gene identification in resulting contigs in attempts to identify homologous loci of genes of interest in species with emerging whole genome shotgun reads. A web server hosting Tracembler is provided at http://www.plantgdb.org/tool/tracembler/, and the software is also freely available from the authors for local installations. | Sequencing | Sequence assembly | Linux | |||
| Trans-ABySS | Trans-ABySS is a software package that is designed to analyze ABySS-assembled whole-genome shotgun transcriptome data. | SNP detection Indel detection RNA-Seq Gene structure | BCCA (academic use) | ||||
| Trimmomatic | A flexible read trimming tool for Illumina NGS data | File reformatting Sequencing quality control Sequence trimming | |||||
| Trinity | Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads. | Sequence assembly (de-novo assembly) | Transcriptome assembly | Java C++ | Linux | ||
| Tripal | Tripal is a collection of open-source, freely-available Drupal modules that serves as a web interface for a GMOD Chado database. It is designed to allow anyone with genomic data to quickly create an online genomic database using community supported tools. Tripal is part of the open-source tool collection available through the Generic Model Organism Database (GMOD) project. | Genomics Genetics | Visualisation | PHP | Open Source | ||
| Tview | tview is a lightweight curses based assembly viewer | Visualisation | C | BSD MIT | |||
| UGENE | UGENE is a free cross-platform genome analysis suite that combines popular bioinformatics tools within a single user friendly interface. | Genomics Sequence analysis Phylogenetics Protein structure analysis | Sequence parsing | C++ | GPLv3 | Linux Windows Mac OS X | |
| UnoSeq | UnoSeq is a Java library to analyze next generation sequencing data (e.g. data generated by Illumina's mRNAseq method) and especially perform expression profiling in organisms where no well-annotated reference genome exists. | Sequence assembly (de-novo assembly) RNA-Seq Transcriptome assembly | Java | ||||
| USeq | Collection of software tools for for both low and high level analysis of next generation, ultra high throughput signature sequencing data from the Solexa, SOLiD, and 454 platforms. Initial emphasis: chIP-seq and RNA-Seq with FDR estimations | ChIP-seq RNA-Seq alignment | Java | BSD | |||
| V-Xtractor | V-Xtractor uses Hidden Markov Models to locate, verify, and extract defined hypervariable sequence segments (V1-V9) from bacterial, archaeal, and fungal small-subunit rRNA sequences. | Metagenomics Sequencing | Statistical calculation | Perl | GPL | UNIX | |
| VAAL | VAAL is a variant ascertainment algorithm that can be used to detect SNPs, indels, and more complex genetic variants. | SNP detection Indel detection Structural variation | Sequence alignment | ||||
| VAAST | Variant Annotation, Analysis and Search Tool | Structural variation | Variant prioritisation | Commercial Freeware | |||
| Variant Effect Predictor | Tool for predicting effects of variants for any genome in Ensembl. The web version is limited to 750 variants, but an API and Perl script are provided as well. | SNP | SNP annotation | Perl | |||
| VariantClassifier | The VariantClassifier is a software tool for hierarchically classifying variants based on the genome annotation that is provided. Instead of looking at a region of the genome and seeing all the features relative to each other on the genomic axis, the VariantClassifier inverts the process so that novel variants can be tested for interest, based on the known features on the genomic axis. Furthermore, our hierarchical classification provides a prioritisation of the variants that should be considered for more intensive study. | SNP | SNP annotation | ||||
| Variation toolkit | A set of C++ tools for the interpretation of VCF data. | Genomics SNP Exome and whole genome variant detection | SNP annotation | C++ | GPLv3 | Linux | |
| VariationHunter | Detection of structural rearrangements | Structural variation | Read mapping Variant calling | C | UNIX | ||
| VARiD | VARiD is a variation detection framework for both color-space and letter-space platforms | Genomics SNP detection Indel detection | Statistical calculation | SNP/indel discovery in any format even combining Colorspace with Letterspace | C | GPLv3 | |
| VarScan | VarScan, an open source tool for variant detection that is compatible with several short read align-ers. | SNP detection | SNP calling | Java | |||
| VCAKE | De novo assembly of short reads with robust error correction. An improvement on early versions of SSAKE. | Sequence assembly (de novo assembly) | Sequence assembly K-mer counting | Perl C | GPL | Linux Mac OS X | |
| Vcflib | API and command line utilities for the manipulation of VCF files. | Genomics | C++ | MIT | |||
| VCFtools | Package for dealing with VCF (variant call format) files. Both command line and Perl API. | C++ | GPLv3 | ||||
| Vectorfriends | VectorFriends is an advanced, integrated, and user-friendly sequence analysis software for molecular biologists. It combines various types of in silico cloning, sequence analysis and data management into a single application. | Sequence assembly Sequence alignment Visualisation Annotation Sequence alignment visualisation | Isothermal Sequence assembly gateway and multisite gateway cloning TOPO PCR cloning restriction cloning cloning history multiple sequence alignment Phylogenetic tree visualization Sanger sequence assembly ORF analysis Translation analysis GC plot analysis | Java | Free for academic use; Commercial | Windows | |
| Velvet | Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD | Sequence assembly (de novo assembly) | Sequence assembly Sequence assembly (de-novo assembly) | GPL | |||
| VelvetOptimiser | VelvetOptimiser is a multi-threaded Perl script for automatically optimising the parameter options for the Velvet de novo sequence assembler. | Sequence assembly (de novo assembly) | Perl | GPLv2 | |||
| Vicuna | De novo assembly of viral populations | Sequence assembly (de novo assembly) Population Genomics Viral genomics | C++ | POSIX | |||
| VIP | A complete package designed for next-generation diagnostics using 454 sequencing. | Genomics SNP | SNP detection Mapping SNP annotation | Read mapping SNP calling coverage analysis SNP annotation | Perl MySQL | LGPL | Linux |
| ViralFusionSeq | Accurately discover viral integration events and fusion transcripts by the use of soft-clipping information, read-pair analysis, and targeted de novo assembly | Sequence assembly (de novo assembly) Genomics Mapping Gene structure | Sequence assembly Read mapping Sequence alignment Read pre-processing | Accurately discover viral integration events and fusion transcripts | Perl | GPLv3 | Linux |
| VirusHunter | Next generation sequencing (NGS) technologies allow us to explore virus interactions with host genomes that lead to carcinogenesis or other diseases; however, this effort is largely hindered by the dearth of efficient computational tools. Here, we present a new tool, VirusHunter, for the identification of viruses and their integration sites in host genomes using any type of existing NGS data. VirusHunter's unique features include the characterization of insertion loci of any type of virus in the host genome and high accuracy and computational efficiency as a result of its well-designed pipeline. | ||||||
| VirusSeq | We developed a new algorithmic method, VirusSeq, for detecting known viruses and their integration sites in the human genome using next-generation sequencing data. We evaluated VirusSeq on RNA-Seq data of 256 TCGA human cancer samples. Using these data, we showed that VirusSeq accurately detects the known viruses and their integration sites with high sensitivity and specificity. VirusSeq can also perform this function using whole genome sequencing data of human tissue. | Genomics Mapping | Read mapping | Perl | Unknown | ||
| VisSR | VisSR (Visualisation of sRNAs): generate a visual representation of sRNAs and user-imported genomic features. | Transcriptomics | Visualisation | Desktop sRNA Visualisation | Java | Custom Licence | Linux 64 Windows Mac OS X |
| Vmatch | A versatile software tool for efficiently solving large scale sequence matching tasks | Read mapping | Commercial | Linux | |||
| WebApollo | WebApollo is a browser-based tool for distributed community annotation of sequences. | Genomics Sequence annotation Sequence functional annotation | Annotation | Real time updating; lazy-loading; sequence visualization; sequence annotation | JavaScript Perl Java | Open Source | Requires Tomcat server |
| WebPrInSeS | WebPrInSeS encompasses two separate software applications. The first is WebPrInSeS-C which performs automated sequence verification of user-defined open-reading frame (ORF) clone libraries. The second is WebPrInSeS-E, which identifies positive hits in cDNA or ORF-based library screening experiments such as yeast one- or two-hybrid assays | Clone verification Protein interactions | browser based | ||||
| WHAM | WHAM is a high-throughput sequence alignment tool. | Read mapping | GPLv3 | ||||
| XMatchView | A visual tool for analyzing cross_match alignments. | Viewer | Python | GPLv3 | Windows Linux | ||
| YASS | YASS is a genomic similarity search tool, for nucleic (DNA/RNA) sequences in fasta or plain text format (it produces local pairwise alignments). | ||||||
| ZINBA | Identifies genomic regions enriched in a variety of ChIP-seq and related next-generation sequencing experiments | ChIP-seq Sequencing | GPLv3 | ||||
| ZOOM | ZOOM (Zillions Of Oligos Mapped) is designed to map millions of short reads, emerged by next-generation sequencing technology, back to the reference genomes, and carry out post-analysis. ZOOM is developed to be highly accurate, flexible, and user-friendly with speed being a critical priority. | Read mapping | Linux Windows | ||||
| ZORRO | ZORRO is an hybrid sequencing technology assembler. It takes to sets of pre-assembled contigs and merge them into a more contiguous and consistent assembly. The main caracteristic of Zorro is the treatment before and after assembly to avoid errors. | Genomics | Sequence assembly | Perl | GPL | Linux |
