Software

Stubs:

App.	Article Size	Article 'Score'
HMMSplicer	172	20
Reconciliator	208	40
CHiPSeq	211	30
MAQGene	215	20
RACA	218	0
Arf	227	0
DiBayes	230	40
CPTRA	232	20
ChIPseqR	232	20
Scripture	233	30
... further results

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	Bioinformatics method	Biological technology	Operating system	Language	Maintained	Licence
.NET BIO			Windows Linux	C#	Yes
4peaks	Sequence analysis	Sanger	Mac OS X		Yes	Freeware
A5	De-novo assembly	Illumina	Linux Mac OS X		Yes	GPLv3
AB Large Indel Tool	Mapping	ABI SOLiD	Linux 64	Perl	No	GPL
AB Small Indel Tool	Read mapping Sequence alignment	ABI SOLiD	Linux 64	Perl C++	Maybe	GPL
ABBA	Sequence assembly Scaffolding		Linux		Maybe	Artistic License
ABMapper	Read mapping Sequence alignment	Illumina	Linux	C++ Perl	Yes	GPLv3
ABySS	Sequence assembly Sequence assembly (de-novo assembly)	Illumina 454 ABI SOLiD Sanger	POSIX Linux Mac OS X	C++	Yes	Commercial Freeware
Adapter Removal (software)	Adapter removal	Illumina 454	Linux 64 Windows Mac OS X	Java	Yes	Custom Licence
ADTEx	Statistical calculation	Illumina	GNU/Linux	Python R	Yes	GPLv3
AGE	Sequence alignment	Illumina			Maybe	Creative Commons license (Attribution-NonCommerical).
AGILE	Mapping	454		C	Yes
Agp2amos	Formatting		Windows Linux		Maybe
Alcovna				Java	Maybe
ALEXA-Seq				Perl	Maybe	GPLv3
ALLPATHS	Sequence assembly Sequence assembly (de-novo assembly)				Yes
Alta-Cyclic	Base-calling	Illumina			No
AMOS	Sequence assembly Sequence assembly validation Integrated solution Formatting Sequence assembly visualisation		Linux	C Perl	Maybe
ANCHOR	Sequence assembly	Illumina	Linux	C++ Python	Yes	BCCA (academic use)
AnCorr	Statistical calculation Correlation	Any	Cross-Platform	Perl C CGI PHP JavaScript	Yes	free for non-commercial academic research
Anno-J	Visualisation				No	Creative Commons - Attribution-NonCommercial-ShareAlike
ANNOVAR	Annotation Variant prioritisation		Linux Windows Mac OS X	Perl	Yes	Commercial Freeware
Arachne	Sequence assembly	Sanger			Maybe
AREM	Read mapping Peak calling	Illumina	Linux	Python	Yes
Arf					Maybe
Array Suite (Array Studio/Server)	Read mapping Gene expression profiling	454 Illumina	Windows	C#	Yes	Commercial
ArrayExpressHTS				R	Maybe
ArrayStar	Statistical calculation Differential expression analysis Ontology comparison Genetic variation analysis	Affymetrix Roche NimbleGen Agilent GenePix Illumina	Windows 7 64-bit or Higher Mac OS X 10.7 10.8 or 10.9 with Parallels Desktop		Yes	Commercial
ASC	Statistical calculation and probability				Maybe
ATAC	Sequence alignment Sequence assembly validation		Linux		Maybe
Atlas Suite	Variant calling	Illumina 454 ABI SOLiD	POSIX	Ruby C	Yes	BSD
Atlas-SNP2			UNIX	Ruby	Yes	Freeware
Avadis NGS	Sequence alignment Visualisation Sequencing quality control Sequence analysis Analysis Biological interpretation	Illumina 454 ABI SOLiD Ion Torrent PacBio Ion proton	Windows Linux Mac OS X	Java R Python	Yes	Commercial
Baa.pl	Sequence assembly validation Sequence alignment analysis	Any	any	Perl	Yes	GPL
Bambino				Java	Maybe
Bambus	Scaffolding				Yes
BAMseek	Sequence alignment visualisation	Any	Cross-Platform	Java	Yes	GPLv3
BamTools	Sequence alignment analysis		Cross-Platform	C++	Yes	MIT
BamView	Visualisation		Mac OS X UNIX Windows	Java	Maybe	GPL
Barcode generator	DNA barcoding	Illumina		Python	Maybe
Barcrawl Bartab	DNA barcoding	454			Maybe	GPL
BarraCUDA	Read mapping Sequence alignment	Illumina ABI SOLiD	Linux	C C++ CUDA	Yes	GPLv3 MIT
Batman				Java	No	LGPL
BayesCall	Base-calling	Illumina		C++ Python	No	GPLv3
BayesPeak	Statistical calculation	Illumina		R	Yes	GPL
BaySeq	Differential expression analysis	Illumina		R	Yes
BBMap	Read mapping Sequence alignment Sequence contamination filtering Sequence trimming RNA-Seq analysis	Sanger Illumina 454 Ion Torrent PacBio	Windows NIX Mac OS X all supporting JVM	Java 7	Yes	BSD
BBSeq				R	Maybe
Bcbio-nextgen	Read mapping Sequence alignment Peak calling Sequence motif recognition Genotyping Sequencing quality control Differential expression analysis Sequence trimming Filtering Genomic region matching		platform-independent	Python	Yes	MIT
BEADS	Standardisation and normalisation	Illumina			Maybe
BEAP	Read mapping				Maybe
BEDTools	Mapping		Linux Mac OS X	C++	Yes	GPLv2
Bedutils					Maybe
Belvu	Sequence alignment visualisation		Linux		Maybe
BFAST	Read mapping Sequence alignment Genome indexing	ABI SOLiD Helicos 454 Illumina	Solaris UNIX	C	Yes	GPL
BFCounter	K-mer counting			C++	Yes	GPLv3
BigBWA	Read mapping Sequence alignment Mapping	Illumina ABI SOLiD SOLiD Ion Torrent Ion proton	Linux 64	Java	Yes	GPLv3
BING	Base-calling Sequencing quality control	Illumina			Maybe
BioJava				Java	Yes	LGPL 2.1
Bionimbus			Linux Amazon EC2 cloud		Yes
BioNumerics	Sequence assembly Read mapping Sequence alignment Annotation Genome visualisation Variant calling Comparative genomics Workflows	Sanger Illumina Ion Torrent PacBio	Windows 7 or Higher		Yes	Commercial
BioPerl			Cross-Platform	Perl	Yes
BioPHP				PHP	Yes	GPLv2
Biopieces	Sequence alignment Visualisation Sequencing quality control Sequence analysis			Perl Python Ruby C	Yes	GPLv2
Biopython	Sequence parsing		Linux Windows Mac OS X	Python	Yes	Biopython License (MIT/BSD style)
BioRuby			Cross-Platform	Ruby	Yes
BioSmalltalk	Sequence parsing		Linux Windows Mac OS X	Smalltalk	Yes
BiQ Analyzer			Windows Linux Mac OS X Solaris	Java	Yes
BiQ Analyzer HT			Windows Linux Mac OS X Solaris	Java	Yes
Bis-SNP	Bisulfite mapping SNP calling Methylation calling	Illumina	Linux Mac OS X	Java Perl	Yes	MIT
Bismark	Read mapping Bisulfite mapping Methylation calling		Linux Mac OS X Windows	Perl	Yes	GPLv3
Bison	Read mapping Bisulfite mapping Methylation calling		Unix-like Linux Mac OS X	C	Yes
BLAST	Sequence analysis		Linux		Yes
BLAST Ring Image Generator	Visualisation Sequence assembly visualisation		Cross-Platform		Yes
BLAT	Read mapping Sequence alignment		Linux Mac OS X	C	Maybe	Freeware
Blixem	Sequence alignment visualisation		Linux		Maybe	GPL
BOAT	Read mapping				Maybe	GPL
Bort		Any	any	Perl	Yes
BOW					Maybe
Bowtie	Read mapping Genome indexing (Burrows-Wheeler)		Mac OS X Linux Windows		Yes
BRAT	Bisulfite mapping Mapping	Illumina			Maybe	GPLv3
BRCA-diagnostic				Perl	Maybe
BreakDancer				Perl C++	Maybe	GPLv3
Breakpointer	Statistical calculation			C++ Perl	Yes	GPL
BreakSeq	Read mapping				Maybe
BreakTrans	Post-analysis				Maybe
Breakway	SNP calling Sequence analysis	ABI SOLiD Illumina 454 Sanger	Linux Mac OS X Windows	Perl	Yes	GPL
BS Seeker	Bisulfite mapping			Python	Maybe
BS-Seq	Bisulfite mapping				Maybe
BSMAP	Read mapping Bisulfite mapping		Linux 64	C++	Maybe	GPLv3
BSSim	Modelling and simulation	Illumina 454 ABI SOLiD	UNIX Linux Mac OS X Windows	Python	Yes	GPLv3
Btrim	Sequence trimming		Linux		Yes
BWA	Read mapping	Sanger Illumina 454 ABI SOLiD	UNIX	C	Yes	GPLv3 MIT
BWA-SW	Read mapping	Sanger Illumina 454	UNIX	C	Yes	GPLv3 MIT
CABOG	Sequence assembly	Sanger 454 Illumina	Linux		Yes
CANGS	Sequencing quality control Sequence trimming Primer removal	454		Perl	Yes
CARPET	Genotyping			C++	No
CASHX	Read mapping				Maybe
CATCH	Sequence alignment Clustering			Java	Yes	Open Source
CatchAll					Yes
CEQer		Any	Windows Mac Linux	C#	Yes	GPLv3
CexoR	Peak calling	Illumina HiSeq 454 ABI SOLiD Ion Torrent Illumina Solexa Illumina	Linux Mac OS X Windows	R	Yes	GPL-2 + file LICENSE
CGA Tools	File reformatting	Complete Genomics	Linux UNIX Mac OS X	C++	Yes	Apache License 2.0
CHiCAGO	Peak calling	Any	Linux OSX	R Python	Yes	Artistic-2.0
ChimeraScan					Maybe
ChIP-Seq (application)	Read mapping Peak calling	Illumina	Linux Mac OS X	C Perl	Yes	GPL
ChIPmeta	Peak calling				Maybe
ChIPMunk	Sequence motif comparison Sequence motif discovery		platform-independent	Java	Yes	Freeware
CHiPSeq	Peak calling				Maybe
ChIPseqR				R	Maybe
Chipster	Read mapping Peak calling Sequence motif recognition Genome visualisation Sequencing quality control Differential expression analysis Sequence trimming Pathway or network analysis Methylation analysis		platform-independent	Java R	Yes	GPLv3
ChromaSig	Sequence motif recognition			Perl C	Maybe
ChromHMM	Statistical calculation			Java	Yes	GPLv3
Circos	Visualisation		Windows Linux	Perl	Yes
CisGenome	Sequence motif recognition Gibbs sampling Integrated solution Data retrieval		UNIX Windows	C C++	Yes
Cistrome				Python	Yes
CLCbio Genomics Workbench	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	454 Illumina ABI SOLiD Helicos Sanger Ion Torrent	Windows Mac OS X Linux	Java C++	Yes	Commercial
Clean reads	Sequencing quality control Sequence trimming			Python	Maybe
CleaveLand				Perl R	Yes	Freeware
CLEVER		Any Illumina	any	C++ Python	Yes	GPLv3
ClipCrop					Maybe
CloudAligner	Read mapping Hadoop		cloud	Java	Maybe	GPL
CloudBurst	Read mapping			Java	No
ClustDB			Linux		Maybe
Cluster Flow	Analysis pipeline		Linux	Perl	Yes	GPLv3
CNANorm	Peak calling Standardisation and normalisation	Illumina	Linux Mac OS X Windows	R Perl	Yes	GPLv2
CNAseg				R	Maybe
CNB MetaGenomics tools		454 Illumina	Linux Unix-like POSIX	Bash Perl Python C	Yes	EU-GPL
CnD				D	Maybe	GPL
CNVer				Perl C++	Yes
CnvHMM		Illumina	Linux		No
CNVkit	Variant calling	Illumina	GNU/Linux Mac OS X	Python	Yes	BSD
CNVnator					Maybe
CNVseq				Perl R	Maybe
CompreheNGSive	Visualisation		Mac OS X Linux	Python Qt	Yes	LGPL
CoNAn-SNV				C	Maybe
ConDeTri	Sequence trimming	Illumina		Perl	Yes
ContEst	Sequencing quality control			Java	Maybe	BSD
Contra		Illumina	Linux 64 Linux	Python R	Yes	GPLv3
Contrail	Sequence assembly Sequence assembly (de-novo assembly) Hadoop				Yes
CopySeq		Illumina	Mac OS X Linux	Java R	Yes
Coral	Sequence error correction			C++	Yes
CORAL (Contig Ordering Algorithm)	Sequence error correction			Java	Maybe
Cortex	Sequence assembly Variant calling			C	Yes	GPLv3
CPTRA				Python	Maybe
CRAC	Read mapping Genome indexing (Burrows-Wheeler)	Illumina 454 Ion Torrent	Linux Linux 64 Mac OS X	C++	Yes	CeCILL
CRAVAT	Annotation Variant prioritisation SNP annotation Variant classification Sequence annotation		Web Linux		Yes
CRISP				Python	Maybe
Crossbow	Read mapping				Yes
CUDA-EC	Sequencing quality control			C	Maybe
Cufflinks	Read mapping Transcriptome assembly Differential expression analysis	Illumina 454 Ion Torrent Illumina HiSeq Illumina Solexa			Yes	Boost
CummeRbund	Visualisation	Illumina			Maybe
Curtain	Sequence assembly Sequence assembly (de-novo assembly)	Illumina 454 ABI SOLiD			Maybe	Apache License 2.0
Cutadapt				Python Cython	Yes	MIT
DCLIP	Sequence alignment analysis	NGS	UNIX Unix-like	Perl C	Yes
DecGPU	Sequence error correction		Linux	C++	Yes	GPLv3
DeconSeq	Sequence contamination filtering	Sanger 454 Ion Torrent PacBio	UNIX Mac OS X	Perl C	Yes	GPLv3
DeepTools	Visualisation Conversion Standardisation and normalisation	Illumina HiSeq 454 Illumina	Linux Mac OS X	Python	Yes	GPLv3
DeFuse					Yes
DEGseq	Differentially expressed gene identification			R	Yes
DESeq	Sequencing quality control Statistical testing		UNIX Windows Mac OS X	R	Yes	GPLv3
DIAL			Linux	C Python	Maybe	MIT
DiBayes					Maybe	GPL
DiffBind	Differential binding sites	Illumina ABI SOLiD 454 Any Illumina HiSeq Illumina Solexa	Linux Mac OS X Windows	R	Yes	Artistic-2.0
Diffreps	Differential Binding	Illumina ABI SOLiD	Linux Windows Mac OS X	Perl	Yes	GPLv3
Dindel	Localised reassembly	Illumina			Maybe
DiscoSnp	Sequence assembly (de-novo assembly) Read depth analysis	All	Unix-like iOS	C++	Yes	CeCILL
DNA Baser	Sequence assembly Sequence analysis Sequence assembly editing	Sanger 454	Windows		Yes	Commercial Freeware
DNA Chromatogram Explorer	File reformatting Chromatogram visualisation	Sanger	Windows		Yes	Freeware
DNAA	Sequencing quality control Modelling and simulation Statistical calculation	ABI SOLiD Illumina 454			Maybe	GPL
DNaseR	Peak calling Nucleic acid sequence feature detection	Illumina HiSeq 454 ABI SOLiD Ion Torrent Illumina Solexa Illumina	Linux Mac OS X Windows	R	Yes	GPL-2 + file LICENSE
DNAzip	File reformatting			C++	Maybe
DrFAST		ABI SOLiD			Maybe
DSAP			browser based		Maybe
DSGseq	Statistical calculation Differential expression analysis RNA-Seq analysis	Illumina 454 ABI SOLiD Ion Torrent	Linux Windows Mac OS X	C R	Yes	Commercial Freeware
DSRC	File reformatting				Maybe
E-miR		Illumina			Maybe
Ea-utils	Sequencing quality control Sequence trimming			C++	Yes	MIT
EagleView	Sequence assembly visualisation				Maybe
EagleView genome viewer	Visualisation		Linux Windows Mac OS X		No
EaSeq	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...	Any HTS	Windows 7 or Higher		Yes	Freeware Custom Licence
Easyfig	Comparative genomics	Any	Windows Mac OS X GNU/Linux	Python	Yes	GPLv3
EBCall					Maybe
ECHO	Sequence error correction			Python C++	Maybe	BSD
EDENA	Sequence assembly				Maybe
EdgeR	Statistical calculation	Illumina ABI SOLiD 454 Any	Windows Mac OS X UNIX	R	Yes	LGPL
ELAND	Sequence alignment				Maybe	Commercial
EMBF	Mapping				Maybe
Epigenome	Bisulfite mapping			R Python	Yes
EpiGRAPH	Statistical calculation		browser based		Yes
ERANGE				Python	Yes
ERDS					Maybe
ERGO Genome Analysis and Discovery System	Sequence alignment SNP detection SNP annotation Gene expression analysis Pathway or network analysis Sequence annotation Sequence functional annotation Metabolic network modelling	Sanger Illumina 454 ABI SOLiD Ion Torrent	Web		Yes	Commercial
ERNE	Read mapping Bisulfite mapping	Illumina	Linux Mac OS X Windows	C++	Yes	GPLv3
Error Correction Evaluation Toolkit	Sequencing quality control	Illumina 454 Ion Torrent	POSIX	Python Perl	Maybe
Est2assembly	Sequence assembly	Sanger 454			Maybe
ESTcalc				Perl	Maybe
EULER	Sequence assembly Sequence assembly (de-novo assembly)		Linux	C++ Perl	Maybe
ExomeCNV				R	Maybe
ExomeCopy			Linux Windows Mac OS X	R	Yes	GPL 2.0+
ExomePicks					Maybe
Exonerate	Sequence alignment	Any	Linux	C	Yes	GPL
FAAST	Read mapping	454	Linux		Maybe
FaBox		all			Maybe
FACS		Any	Linux	Perl f	Yes	GPLv2
Falcon	Sequence assembly	PacBio			Yes
FAST: Fast Analysis of Sequences Toolbox	Sequence analysis Sequence parsing		GNU/Linux Mac OS X		Yes
FastQ Screen	Read mapping Sequencing quality control	Illumina ABI SOLiD	Linux Mac OS X Windows	Perl	Yes	GPLv3
FastQC	Sequencing quality control	Illumina ABI SOLiD	UNIX Windows	Java	Yes	GPLv3
FastQValidator	Sequencing quality control			C++	Maybe
FDM					Yes
FeatureCounts	Read summarisation	Illumina 454 ABI SOLiD Ion Torrent	Linux 64 Mac OS X Mac OS X; x86 64	R C	Yes	GPLv3
FHiTINGS	Sequence alignment		Cross-Platform	Python	Yes
Figaro	K-mer counting	Sanger	UNIX	C++ Perl	Maybe	Artistic License
Filter	Sequence contamination filtering	Illumina 454	Linux 64 Windows Mac OS X	Java	Yes	Custom Licence
FindPeaks 3.1	Peak calling	Illumina			Yes	GPLv3
FindPeaks 4.0 (Vancouver Short Read Package)	Peak calling Formatting Sequence alignment analysis		Linux Windows Mac OS X	Java	Yes	GPL
FLASH	Sequence assembly Read pre-processing		Linux 64	C	Maybe	Open Source
Flexbar	Adapter removal Sequence trimming DNA barcoding Quality control Read pre-processing	Illumina 454 ABI SOLiD	Linux Windows Mac OS X	C++	Yes	GPLv3
Flower		Ion Torrent 454		Haskell	Maybe
FlowSim	Sequence error correction Modelling and simulation	454		Haskell	Maybe
Flux	Modelling and simulation				Maybe
Forge	Sequence assembly				Yes
FragGeneScan				C Perl	Maybe	GPL
FrameDP					Maybe
FreClu	Read mapping				Maybe
Freebayes					Yes	MIT
FREEC			Linux Linux 64 Windows		Maybe
FusionAnalyser		Illumina	Windows Linux	C#	Yes	GPLv3
FusionCatcher	Sequence alignment	Illumina HiSeq/NextSeq/MiSeq/Solexa	NIX	Python	Yes	GPLv3
FusionHunter			Linux Linux 64	Perl C	Maybe
FusionMap	Split-read mapping		Windows Linux Linux 64	C#	Yes	Commercial Freeware
FusionSeq	Sequence alignment analysis	Any	Mac OS X UNIX Linux	C	Yes	Creative Commons - Attribution; Non-commercial 2.5
Fuzzypath	Sequence assembly Sequence assembly (de-novo assembly)				Maybe
G-Mo.R-Seq			Linux		Yes	CeCILL
G-SQZ	File reformatting			C++	Maybe
Galaxy	Sequence assembly Sequence alignment Visualisation Sequencing quality control		Cross-Platform	Python	Yes
Galign	Read mapping	Illumina			Maybe	GPL
Gambit	Visualisation				Yes	GPL 2.0+ Commercial
GAMES	SNP detection Indel detection SNP annotation	Illumina	Linux	Perl	Maybe
GASSST	Sequence alignment Mapping		Linux	C++	Yes	CeCILL
GASV					Yes	GPLv3
GATK	Localised reassembly Statistical calculation			Java Python	Yes
GBrowse	Visualisation	Any	Linux Mac OS X Windows	Perl	Yes	Open Source
GeeFu	Sequence assembly			Ruby	Maybe
GEM	Peak calling Sequence motif discovery	Illumina HiSeq Illumina Solexa	Cross-Platform	Java	Yes	Commercial Freeware
GEM library	Read mapping			C Python OCaml	No	GPLv3
GENALICE MAP	Read mapping Variant calling	Illumina HiSeq X Ten	Linux		Yes	Commercial
GENE-Counter			Linux Mac OS X		Yes
Genedata Expressionist	Read mapping Sequence alignment Annotation Bisulfite mapping Clustering Genome visualisation Sequencing quality control Sequence analysis Statistical calculation Gene expression analysis RNA-Seq analysis	Any	Windows Linux	Java	Yes	Commercial
Geneious	Sequence assembly Read mapping Sequence alignment Visualisation Annotation Sequence assembly validation Genome visualisation Variant calling DNA barcoding Sequence motif discovery	Sanger Illumina ABI SOLiD 454	Windows Mac OS X Linux Solaris	Java	Yes	Commercial
GeneProf	Read mapping Visualisation Peak calling Sequencing quality control Differential expression analysis	Illumina Illumina HiSeq Illumina Solexa	browser based	Java JavaScript	Yes	Commercial Freeware
GeneTalk	Annotation Sequence contamination filtering Sequence analysis Variant calling Genetic variation analysis Plotting and rendering Exome analysis Variant classification			Ruby JavaScript	Yes	Freemium
Genomatix Mining Station (GMS)	Sequence assembly Read mapping SNP calling Correlation	Illumina ABI SOLiD Helicos 454	Windows Mac OS X Linux	C++ Java Flash	Yes	Commercial
Genome Trax		Illumina 454 ABI SOLiD			Yes	Commercial
GenomeBrowse	Visualisation Sequence assembly visualisation Sequence alignment visualisation	Illumina ABI SOLiD Sanger 454 Ion Torrent	Windows Linux Mac OS X		Yes
Genomedata	Signal	Any	Linux Mac OS X	Python C	Yes	GPL
GenomeJack	Visualisation	Sanger Illumina 454 ABI SOLiD	Windows Mac OS X Linux	Java	Yes	Freeware
GenomeMapper	Read mapping Sequence alignment				Maybe
Genometa	Read mapping Visualisation	Any	Linux Mac OS X Windows	Java	Yes
GenomeTools			POSIX Linux Mac OS X OpenBSD Windows (Cygwin) UNIX	C	Yes	BSD
GenomeView	Visualisation Data retrieval Genome visualisation Sequence alignment visualisation Plotting and rendering	Any	platform-independent	Java	Yes	GPL
GenomicTools	Peak calling Heat map generation Genome comparison			C C++	Yes	GPLv2
GenoMiner	Sequence assembly Sequence alignment Peak calling Sequence error correction Plotting and rendering Mutation detection Gene expression profiling	Any	Linux	Java	Yes	Commercial
GenoREAD	Sequence assembly Read mapping Sequence alignment	Sanger	Linux 64	Perl PHP JavaScript	Yes
GenoViewer	Viewer	Any	platform-independent	Java	Maybe	Freeware
GensearchNGS	Sequence alignment Sequence alignment visualisation Read alignment Variant prioritisation Mutation detection	454 Illumina Ion Torrent	UNIX Windows	Java	Yes	Commercial
GenVision	Visualisation		Windows Mac OS X		Yes	Commercial
Geoseq	Read mapping				Yes
GigaBayes	SNP calling				No
GimmeMotifs	Sequence motif comparison	Any	Linux	Python	Yes	MIT
Girafe	Sequence alignment			R	Maybe
Gk arrays	Sequence assembly Read mapping Sequence error correction	Illumina 454 Sanger	Linux Linux 64 Mac OS X any	C++	Yes	CeCILL-C license
GlobalSeq	Omnibus test Global test Joint significance test		cross-platform	R	Yes	GPL-3
GMAP	Read mapping Sequence alignment		UNIX	C Bourne shell	Yes
Gnumap	Read mapping	Illumina		C++	Yes
Goby framework	File reformatting	Illumina ABI SOLiD 454		Java	Yes	GPLv2
Golden Helix	Annotation Genome visualisation Sequencing quality control Sequence contamination filtering Variant calling Statistical calculation Collapsing methods Variant classification	Illumina Ion Torrent Affymetrix Complete Genomics Sanger Agilent Roche NimbleGen ABI SOLiD	Windows Linux Mac OS X		Yes
Goseq	Gene set testing	Illumina ABI SOLiD	UNIX Windows	R	Yes	LGPL
Gowinda	Ontology comparison Functional enrichment Genome-wide association study		Mac OS X Linux Windows	Java	Yes	Mozilla Public License
GPS	Peak calling		Cross-Platform	Java	Yes	Commercial Freeware
GPSeq				R C	Maybe
GRIDSS	Sequence assembly Split-read mapping Read alignment Assembly Whole genome breakend assembly	Illumina	Cross-Platform	Java	Yes	GPLv3
GRS	File reformatting		Linux Linux 64	C Bourne shell	Maybe	Commercial Freeware
GSNAP	Read mapping Bisulfite mapping			C Perl	Maybe
Hairpin Annotation		Illumina 454	Linux 64 Windows Mac OS X	Java	Yes	Custom Licence
Haplowser	Visualisation Haplotype inference	Any		Java	No	GPL
HawkEye	Sequence assembly visualisation		Linux Mac OS X	C++	Yes	Artistic License
HeliSphere	Mapping	Helicos	Linux		Yes	Freeware
HI	Haplotype reconstruction	Illumina		Java	No
Hicup	Read mapping	Illumina Ion Torrent	UNIX Linux Mac OS X	Perl	Yes	GPLv3
HINT	Peak calling Nucleic acid sequence feature detection	all	Unix-like	Python	Yes	GPLv3
HiPipe	Read mapping Variant calling Workflows	Sanger Illumina 454 ABI SOLiD Ion Torrent	platform-independent	JavaScript Java Bash	Yes
HiTEC	Sequence error correction	Illumina	Linux	C++	Yes	GPLv3
HMMSplicer				Python	Maybe
HPeak					Maybe
HTSeq				Python	Yes	GPLv3
Hybrid-SHREC	Sequence error correction	Illumina 454 ABI SOLiD		Java	Maybe
IBD2				R Java	Maybe
Ibis	Base-calling		Linux Windows (Cygwin)	Python C C++	Yes	Non-commercial
ICORN	Sequence assembly Sequencing quality control				Maybe
IDBA	Sequence assembly	Illumina	POSIX Linux Linux 64		Maybe
IGV	Visualisation		Windows Mac OS X Linux	Java	Yes	LGPL
Illuminate	Sequencing quality control	Illumina Illumina HiSeq	Unix-like	Python	Yes	MIT
Illuminator		Illumina			Yes
IMAGE	Sequence assembly editing	Illumina			No
Inchworm		Illumina			Maybe
InGAP	Read mapping Sequence assembly visualisation				Maybe
Ingenuity Variant Analysis	Variant classification	Any			Maybe
Integrated Genome Browser	Visualisation	Sanger Illumina Affymetrix 454	platform-independent	Java	Yes	Open Source
Iobio	Visualisation	Any			Yes
IOmics	Sequence assembly Sequence alignment Ab-initio gene prediction Variant calling MiRNA analysis Exome analysis	Illumina	cloud		Yes	Commercial
IQSeq				C++	Maybe
ISAAC			Linux 64	C++	Yes
Isas	Sequence alignment		Linux		Yes
IsoEM	Expectation Maximisation			Java	Maybe
ISSAKE	Sequence assembly	Illumina		Perl Python	No	GPLv2
JBrowse	Visualisation		browser based	Perl JavaScript	Yes	Open Source
Jellyfish			Linux 64 Mac OS X	C++	Maybe	GPLv3
JointSLM				R	Maybe
KARMA	Read mapping	ABI SOLiD 454 Illumina			Maybe
KBASE	Annotation		Linux		Yes
Kismeth	Bisulfite mapping				Maybe
Kissnp	Sequence assembly Sequence assembly (de-novo assembly) Data retrieval	Illumina 454	Linux	C	Yes	CeCILL
Kmergenie	Sequence assembly	Illumina		C++ Python R	Yes
KNIME	Workflows		Windows Mac OS X Linux		Maybe	GPLv3
Knime4Bio	Data retrieval		any	Java	Yes	GPLv3
Krona	Visualisation		Linux UNIX Mac OS X	JavaScript Perl	Yes
Lab7	Workflows	Any	Mac OS X Linux	Python JavaScript	Yes	Commercial
Lasergene	Sequence assembly Read mapping Sequence alignment Peak calling Annotation Sequence analysis Scaffolding Sequence alignment analysis Chromatogram visualisation PCR primer design	454 Sanger	Windows XP Windows 7 or Higher Mac OS X 10.7 10 8 or 10.9		Yes	Commercial
LAST	Sequence alignment			C++	Yes	GPLv3
LASTZ	Read mapping Sequence alignment		Mac OS X Linux		Maybe
LobSTR	Repeat sequence organisation analysis	Illumina	UNIX	C++ R Python	Yes	Freeware
LOCAS	Sequence assembly		Linux	C++	Maybe
LookSeq	Sequence assembly visualisation				Maybe
LSKB, Life Science Knowledge Bank	Annotation SNP calling Sequence analysis Differential expression analysis Pathway or network analysis Classification Analysis pipeline Functional analysis				Yes
MACS	Peak calling		platform-independent	Python	Yes	Artistic License
MagicViewer	Visualisation SNP calling	Illumina	platform-independent	Java	Yes
MapDamage	Sequencing quality control Statistical calculation	Illumina	Linux Mac OS X	Python R	Yes
MapNext	Sequence alignment			C++ Perl	Maybe
Mapsembler	Sequence assembly Read mapping	Illumina 454	Linux	C	Yes	CeCILL
MapSplice	Mapping		Linux	C++ Python	Yes
MapView	Visualisation		Linux Windows		No
MAQ	Read mapping			C++ Perl	No	GPL
MAQGene	Read mapping Integrated solution				Maybe
MARGARITA					Maybe
Mason	Sequence assembly Mapping Modelling and simulation	Illumina 454 Sanger	UNIX Windows	C++	Yes	GPLv3
Mauve	Visualisation Sequence assembly validation Sequence alignment comparison	Any	Mac OS X Windows Linux	C++ Java	Yes	GPL
MAXIMUS	Sequence assembly	Any			Yes
MAYDAY	Visualisation				Maybe
Meerkat		Illumina			Maybe
MEGAN					Maybe	Commercial Freeware
Megraft	Sequence analysis	454 ABI SOLiD Illumina Ion Torrent Sanger	Linux UNIX Mac OS X	Perl	Yes	GPLv3
Meraculous	Sequence assembly			Perl C	Maybe
METAGENassist	Visualisation Statistical calculation Sequence clustering				Yes
Metagenome@Kin	Species frequency estimation Statistical analysis				Yes
MetaSim	Sequence assembly Mapping Modelling and simulation	454 Illumina Sanger		Java	Maybe	Commercial Freeware
Metaxa	Sequence analysis Hidden Markov Model	454 ABI SOLiD Illumina Ion Torrent Sanger	Linux UNIX Mac OS X	Perl	Yes	GPLv3
MethMarker			Windows Linux Mac OS X Solaris	Java	Yes
Methpipe	Bisulfite mapping	Illumina Illumina HiSeq Illumina Solexa	Linux Mac OS X	C++	Yes	GPL (>= 3)
MethylCoder	Read mapping Bisulfite mapping	Illumina	Linux Linux 64 Mac OS X	Python C	Yes	BSD
MetMap					Maybe
MeV	Visualisation Differential expression analysis Sequence clustering Classification				Yes	Artistic License
MG-RAST	Annotation	Sanger 454 Ion Torrent PacBio Illumina	UNIX	Perl C GO JavaScript Python	Yes
MicroRazerS	Read mapping		Linux	C++	No
Microsoft Biology Foundation				C#	Maybe
MICSA	Sequence motif comparison				Maybe
Minia	Sequence assembly	Illumina	Linux Mac OS X	C++	Yes	CeCILL
MIP Scaffolder	Scaffolding	ABI SOLiD Illumina	Linux	C++ Perl	Yes
MIRA	Sequence assembly Read mapping Local sequence alignment K-mer counting Graph reduction Learning algorithm	Sanger Illumina 454 PacBio Ion Torrent	Linux Mac OS X UNIX	C++	Yes	GPL
MiRanalyzer			browser based	Java Perl	Maybe
MiRCat	MicroRNA detection	Illumina 454	Linux 64 Windows Mac OS X	Java	Yes	Custom Licence
MiRDeep		Illumina 454		Perl	Yes
MiRNAkey		Illumina	Linux Mac OS X	Java Perl	No
MiRProf	MicroRNA detection	Illumina 454	Linux 64 Windows Mac OS X	Java	Yes	Custom Licence
MiRspring				Perl JavaScript	Yes	GNU
MirTools		Illumina 454		Perl PHP	Yes
MirTrios	Read mapping Variant calling De novo mutation detection	Any sequencing platform	Linux	Perl PHP JavaScript	Yes
MISO		Any			Yes
Mlgt	Sequence error correction Sequence contamination filtering Sequence analysis Read alignment DNA barcoding	454	Windows UNIX Mac OS X	R	Yes	GPL >=2
MMSEQ			Mac OS X Linux 64	C++	Yes
MochiView	Genome visualisation Sequence motif comparison		Linux Mac OS X Windows	Java	Maybe
MoDIL		Illumina		Python	Yes
MOM	Read mapping	Illumina			No
MOSAIK	Sequence assembly		Windows Linux Mac OS X	C++	Yes	Commercial GPLv2
MotifLab	Visualisation Peak calling Genome visualisation Sequence contamination filtering Sequence motif discovery Format conversion		platform-independent	Java	Yes	Freeware
MPscan	Read mapping	Illumina	Linux Mac OS X	C++	Maybe
MrBayes	Statistical calculation		Cross-Platform		Yes
MrCaNaVaR	Read depth analysis	Illumina	POSIX	C	Yes	Commercial Freeware
MrFAST	Read alignment	Illumina	UNIX	C	Yes	BSD
MrsFAST	Mapping Read alignment	Illumina	UNIX	C	Yes	BSD
MTR				C++ Matlab	Maybe
MU2A	SNP annotation		Windows Linux Mac OS X	Java	No	Apache License 2.0
MultiPSQ	Peak calling Classification Peptide mass fingerprint	Pyrosequencing (QIAGEN)	Windows Linux	C++	Maybe	LGPLv3
MultiQC	Quality control	Any	Windows Mac OS X Linux	Python	Yes	GPLv3
MUMmer	Read mapping Sequence alignment	Any	Linux		Yes	Artistic License
MUMmerGPU	Sequence alignment	Any			Maybe
MuMRescueLite	Mapping			Python	No	MIT
MuSICA 2	Sequence assembly			Perl	Maybe
Mutascope	Variant calling Analysis pipeline	Illumina ABI SOLiD MiSeq	UNIX	Perl	Yes
MuTect	SNP calling				Maybe
Myrialign	Read mapping Sequence alignment				Maybe
Myrna					Maybe
Mzip	File reformatting				Maybe
NarrowPeaks	Peak calling Differential Binding	Illumina HiSeq 454 ABI SOLiD Ion Torrent Illumina Solexa Illumina	Linux Mac OS X Windows	R	Yes	Artistic-2.0
NCBI Genome Workbench	Visualisation Genome visualisation		Cross-Platform		Yes
Nephele	Functional analysis Taxonomic profiling Metagenomic Assembly	Roche Illumina			Yes
Nesoni	Sequence alignment	Illumina 454 ABI SOLiD		Python	Yes
Newbler	Sequence assembly Read mapping	454 Sanger Ion Torrent	Linux 64	C++	Yes	Unknown
Nexalign	Read mapping	454 ABI SOLiD Illumina	UNIX	C++ R	No	GPL
NextGen Utility Scripts		454 Illumina ABI SOLiD			Yes
NextGENe		Illumina 454 ABI SOLiD	Windows	C++	Yes	Commercial
Ngs backbone	Sequence assembly Read mapping	Sanger Illumina 454	UNIX		Yes	AGPL
NGS-DesignTools	Haplotype inference Modelling and simulation				Maybe
Ngs-pipeline	Read mapping Sequence annotation	Illumina ABI SOLiD	Linux	Perl	Yes	GPLv3
Ngs.plot	Visualisation	Any sequencing platform	All	R Python	Yes	GPL (>= 3)
NGSUtils	Formatting Sequencing quality control Sequence contamination filtering Variant calling Read pre-processing	Illumina ABI SOLiD	Linux Mac OS X	Python	Yes	GPL
NGSView	Sequence assembly visualisation				Maybe
NOISeq	Differential expression analysis	Any			Maybe
NovelSeq	Sequence assembly Read mapping Variant calling	Illumina	UNIX	C	Yes	BSD
Novocraft	Read mapping	Illumina ABI SOLiD Helicos	Mac OS X Linux 64	C++	Yes	Commercial Freeware
NPS				Python	No
NucleR	Peak calling Annotation	Illumina 454 SOLiD Ion Torrent Illumina HiSeq	Cross-Platform	R	Yes	LGPLv3
Oases		Illumina ABI SOLiD 454		C	Yes	GPLv3
Oasis	Read mapping Differential expression analysis	Illumina	all supporting JVM	JavaScript Perl Java Python Bash C	Yes
ODIN	Peak calling	NGS	tested for Linux (Ubuntu)	Python	Yes
OLego	Read mapping Sequence alignment	Illumina	Linux Linux 64 Mac OS X	C++	Yes	GPLv3
Omixon Variant Toolkit	Sequence assembly Read mapping Sequence alignment	Illumina Ion Torrent ABI SOLiD 454	interoperable		Yes	Commercial Freeware
Optimus Primer	PCR primer design				Maybe
PacBio conversion tools	File reformatting	PacBio		Java R Python	Yes
PaCGeE	Read mapping				Maybe	Commercial
PALMA	Sequence alignment				Maybe
PALMapper	Read mapping			C++	Yes	GPLv3
PanGEA		454		Perl	Maybe	Mozilla Public License
PARalyzer				Java	Maybe	Commercial Freeware
Partek Genomics Suite					Yes
PASH	Sequence alignment Bisulfite mapping				Maybe
PASS	Sequence alignment		Linux Windows	C++	Maybe
Patchwork		ABI SOLiD Illumina Complete Genomics	Linux Mac OS X	R	Yes
PatMaN	Read mapping				Maybe
PE-Assembler	Scaffolding			C++	Yes
PeakAnalyzer				Java C++ R	Yes
PeakRanger	Peak calling		Linux Mac OS X	C++	Yes	Artistic License
PeakSeq				C Perl	Maybe
PeakTrace	Base-calling	Sanger	Windows Mac OS X Linux 64	C	Yes	Commercial
PECAN	Sequence alignment				No
PEMer					Maybe
PERalign			Linux	C++	Maybe
PerM	Read mapping	Illumina ABI SOLiD	Linux	C++	Yes	Apache License 2.0
Phred	Base-calling	Sanger	Solaris IRIX AIX	C	Maybe
Phred Phrap Consed Cross match	Sequence assembly Sequence alignment Base-calling Local sequence alignment	Sanger			Yes
Phymm					Maybe
PiCall				C	Maybe
PICS				R	Maybe
PileLine	Plotting and rendering			Java	Maybe	LGPL
Pindel	Read mapping Split-read mapping Localised reassembly	Illumina	Linux Mac OS X Windows	C++	Yes
Pipeline Pilot	Read mapping Sequence alignment Sequence analysis Variant calling Comparative genomics Gene expression analysis	Sanger Illumina 454 ABI SOLiD	Linux Windows	C++ Java Perl R Pilot Script	Yes	Commercial
PIQA	Sequencing quality control	Illumina		R	Maybe
PoissonSeq	Differential expression analysis	Any			Yes
PolyBayesShort			Linux Linux 64		Maybe
PoolHap	Read mapping Regression analysis				Yes
PoPoolation				Perl R	Maybe
PoPoolation2				Perl R	Maybe
Post Assembly Genome Improvement Toolkit	Sequence assembly validation		Linux		Yes
Precrec			Windows Mac OS X Unix-like	R	Yes	GPL-3
PRICE	Sequence assembly			C++	Yes
PRINSEQ	Sequence contamination filtering Sequence trimming Read pre-processing	Sanger Illumina 454 Ion Torrent PacBio	UNIX Mac OS X Windows	Perl	Yes	GPLv3
ProbeMatch	Mapping	Illumina	Linux Mac OS X		No
ProbHD				Perl R Python	No
Promisec Endpoint Manager	Security Endpoint Management Remediation				Maybe
Proxygenes	Read mapping Annotation				Maybe
Pybedtools	Read mapping		Windows (Cygwin) Linux Linux 64 Mac OS X	Python	Yes	GPLv2
PyroBayes	Base-calling	454			No
PyroMap	Read mapping			Python	Maybe
PyroNoise		454			Maybe
QCALL					Maybe
Qpalma	Sequence alignment	Illumina 454		Python C++	Maybe
QRidge	Sequence assembly	Any sequencing platform			Maybe
QSeq	Sequence alignment Visualisation Peak calling	Roche NimbleGen Illumina 454 ABI SOLiD Helicos Sanger	Windows 7 64-bit or Higher Mac OS X 10.7 10.8 or 10.9 with Parallels Desktop		Yes	Commercial
QSRA	Sequence assembly				No
QuadGT	SNP calling Variant calling	Any		Java	Yes
Quake	Sequence error correction	Illumina			Maybe
QualiMap	Sequencing quality control			Java R	Maybe
QUAST	Visualisation Sequence assembly validation	Any	Linux Mac OS X	Python C Perl	Yes	GPLv2
QuEST				C++	No	GPLv2
Quip	File reformatting		any	C	Yes	BSD (3-clause)
R2R	Sequence alignment			Perl	Maybe
R453Plus1Toolbox		454		R	Yes
RACA					Maybe
RApiD				Perl C++	Maybe	GPLv3
RAPSearch	Sequence alignment			C++	Yes	GPLv3
RAST	Genomics Annotation				Yes
Ray	Sequence assembly	Illumina 454	Linux POSIX	C++	Yes	GPL
RazerS	Read mapping Local sequence alignment	Sanger Illumina 454	UNIX Mac OS X Windows	C++	Yes	GPLv3
RDiff	Sequence alignment Differential expression analysis	Illumina HiSeq Illumina Solexa Illumina	Linux Mac OS X	Python Matlab	Yes	Open Source
RDP Pyrosequencing Pipeline	Sequence alignment Formatting	454	browser based		Maybe
Readaligner	Read mapping				Maybe
ReadDepth				R	Maybe	Apache License 2.0
REAL	Mapping		Linux	C++	Maybe	GPLv3
Reaper	Adapter removal Sequencing quality control Sequence contamination filtering Sequence trimming DNA barcoding	Illumina 454	Linux UNIX Mac OS X	C	Yes	GPLv3
... further results