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	Bioinformatics method	Biological technology	Operating system	Language	Maintained	Licence
Reconciliator	Sequence assembly		Linux	Perl	Maybe
RECOUNT	Expectation Maximisation	Illumina	Linux	C++	Yes	GPL
RefCov					No
Repitools	Visualisation Sequencing quality control Statistical calculation Methylation calling			R	Yes	LGPL
Reptile	Sequencing quality control	Illumina		C++	Yes	GPL Boost
ReSeqSim	Read mapping Simulation				Maybe
RGA	Sequence assembly	Illumina			Maybe
RiboPicker	Read pre-processing RRNA filtering	Sanger Illumina 454 Ion Torrent PacBio	UNIX Mac OS X	Perl C	Yes	GPLv3
RMAP	Read mapping Bisulfite mapping		Linux Mac OS X		Maybe	GPLv3
RNA	Read mapping	Illumina ABI SOLiD 454	Linux UNIX Windows Mac OS X	C++	Yes	GPLv3
RNA-MATE					Maybe
RNASEQR	Read mapping				Maybe
Rnnotator					Maybe	Commercial Freeware
RobiNA	Differential expression analysis	Illumina	Windows Linux Mac OS X	Java R	Yes	GPL
Rolexa	Base-calling			R	Maybe
RSAT peak-motifs	Sequence motif recognition Sequence motif comparison Sequence motif discovery	Any	UNIX Mac OS X Linux	Perl CGI Python C	Yes	Commercial Freeware
RSEM				C++	Maybe
RSEQtools			Mac OS X UNIX Linux	C	Yes	Creative Commons - Attribution; Non-commercial 2.5
Rsolid	Base-calling	ABI SOLiD		R C	Maybe
Rsubread	Read mapping Read summarisation Quality assessement	ABI SOLiD Illumina HiSeq Illumina Solexa Ion Torrent 454	Linux 64 Mac OS X; x86 64 Mac OS X	R C	Yes	GPLv3
RTG	Read mapping Sequence alignment K-mer counting Sequence contamination filtering Read depth analysis Translated nucleotide search Species frequency estimation	Illumina Ion Torrent Complete Genomics 454	Linux Mac OS X Windows		Yes	Commercial free for non-commercial academic research
RUbioSeq	Variant calling	Illumina ABI SOLiD	UNIX	Perl	Yes
S-MART			Linux Mac OS X Windows	Python Java	Yes
SAMMate	Sequence analysis		Windows Mac OS X	Java	Yes	GPLv3
Samscope	Read mapping Visualisation	Any	POSIX Linux	C++	Yes	AGPL
SAMStat	Sequencing quality control	Illumina Helicos 454	UNIX	C	Maybe	GPLv3
SAMtools	Sequence assembly visualisation Modelling and simulation			C	Yes	MIT
Savant Genome Browser	Visualisation Sequence alignment visualisation	Illumina 454 Sanger	Windows Linux all supporting JVM Mac OS X	Java	Yes	Apache License 2.0
Scaffolder	Scaffolding		Linux Mac OS X	Ruby	Yes	MIT
ScaffViz	Sequence assembly	454 Illumina Anything that can be assembled with Celera or Newbler			Maybe
SCALCE	File reformatting	Illumina	Linux 64 Linux	C	Yes
SCARF	Sequence assembly				Maybe	GPLv3
Scripture		Illumina			Maybe
SEAL	Read mapping	Illumina		Python C++ Java	Yes	GPLv3
SEECER	Sequence error correction	Illumina 454 Ion Torrent PacBio		C	Yes
SEED	Sequence clustering	Illumina	Mac OS X Linux Windows	C++	Yes
Segemehl	Mapping			C C++	Maybe
Segtor	Annotation SNP annotation		Linux Mac OS X	Perl C	Maybe	Non-commercial
Seq2HLA	Read mapping Genetic variation analysis	Illumina	Unix Mac OS X	Python R	Yes
SeqAn		Sanger Illumina 454	UNIX Mac OS X Windows	C++	Yes	BSD (3-clause)
SeqBuster	Read mapping Annotation	Illumina 454	Mac OS X Linux	Java R	Yes	Commercial Freeware
SeqCons	Sequence assembly		Linux Windows		No
SeqEM	Expectation Maximisation				Maybe
SeqGSEA	Statistical calculation Functional enrichment Functional analysis	Any	any	R	Yes	GPL (>= 3)
SeqMan NGen	Sequence assembly Read mapping Sequence alignment	Ion Torrent Roche 454 Pacific Biosciences Illumina Sanger	Windows 7 64-bit or Higher Mac OS X 10.7 10.8 or 10.9 Linux Ubuntu 12.04 Linux CentOS 6.5		Yes	Commercial
SeqMap	Read mapping		Mac OS X Windows Linux		Maybe
SeqMINER		Any	platform-independent	Java	Yes	GPLv3
SeqMonk	Visualisation Sequence assembly visualisation Sequence alignment visualisation Statistical calculation		Windows Mac OS X Linux	Java	Yes	GPLv3
SeqPrep		Illumina	POSIX	C	Yes	MIT
SeqSaw	Read mapping Sequence alignment	Illumina	Linux	C++	Yes	GPL
SeqSeg				Matlab	Maybe
SeqSite	Peak calling	Illumina HiSeq 454 ABI SOLiD Ion Torrent Illumina Solexa Illumina	Linux Mac OS X Windows	C C++	Yes	GPL
SeqSolve	Ab-initio gene prediction Differential expression analysis Quality control	Illumina ABI SOLiD 454 Ion Torrent Helicos PacBio Any Illumina HiSeq Illumina Solexa	Windows Linux		Yes	Commercial
SeqSphere+	Sequence assembly Read mapping Variant calling	Sanger Illumina 454 Ion Torrent PacBio	Windows Linux 64	Java	Yes	Commercial
SeqTrim	Sequence trimming				Maybe
Sequedex	Sequence analysis Sequence annotation	Illumina HiSeq Illumina Solexa Illumina	Linux 64 Mac OS X	Java Python	Yes	Commercial Freeware
SequenceVariantAnalyzer	Annotation SNP calling Genome visualisation		Linux 64	Java	Yes
Sequencher	Sequence assembly Sequence alignment	454 Illumina ABI SOLiD Ion Torrent Sanger	Windows Mac OS X		Yes	Commercial
SeqWare	Laboratory information management Workflows		Linux	Java	Yes	GPLv3
SeqWords	K-mer counting			Perl	Maybe	Perl artistic licence
SESAME			Windows Linux		Maybe	GPLv3
SEWAL		Illumina			Maybe
Sff2fastq	Conversion	454	Linux		Yes
SGA	Sequence assembly	Illumina	Linux	C++	Yes	GPLv3
SHARCGS	Sequence assembly		Linux	Perl	Maybe
SHE-RA	Sequence error correction	Illumina			Maybe	Open Source
Sherman	Modelling and simulation	Illumina ABI SOLiD	Linux Mac OS X	Perl	Yes	GPLv3
ShoRAH	Read mapping Haplotype inference	454 Illumina	Linux Mac OS X		Yes	GPLv3
Shore	Mapping	Illumina ABI SOLiD	Linux Mac OS X POSIX		Yes
SHOREmap		Illumina ABI SOLiD		Perl R	Yes	GPLv3
ShortFuse				C++ Python	Maybe
ShortRead				R	Yes
SHORTY	Sequence assembly	ABI SOLiD		C++ Perl	No
SHRAP	Sequence assembly				Maybe
SHREC	Sequencing quality control Sequence error correction	Illumina		Java	Yes
SHRiMP	Read mapping	ABI SOLiD Helicos 454 Illumina			Maybe
Sibelia	Variant calling			C++	Yes	GPL
SICER	Sequence contamination filtering			Python	Yes
SiLoCo	Gene expression profiling	Illumina 454	Linux 64 Windows Mac OS X	Java	Yes	Custom Licence
Sim4cc	Read mapping		UNIX Linux	C++	Yes	GPLv2
SimNext	Modelling and simulation	Illumina		Perl	No
SimSeq	Modelling and simulation	Illumina	POSIX	Java C	Yes	MIT
Sissrs	Peak calling		Linux UNIX	Perl	Maybe
Skewer	Read mapping Adapter removal Sequence trimming Read pre-processing	Illumina Illumina HiSeq Illumina Solexa	Linux 64	C++	Yes
Slider	Mapping	Illumina		Java	Maybe
SlideSort	Clustering		Linux Windows	C++	Yes
SLOPE				C++	Maybe
SmashCommunity		454 Sanger			Maybe
SNIP-Seq				Python	Maybe
Sniper			UNIX Mac OS X	C Python	Maybe
SNP-o-matic	Read mapping	Illumina		C++ C	Maybe
SNPsea	Enrichment		NIX	C++ R Python	Yes	GPLv3
SNPSeeker		Illumina		C	No
SNVer			Windows Linux Mac OS X	Java	Maybe
SNVMix				C	Maybe	MIT
SOAP	Read mapping Sequence alignment Genome indexing (Burrows-Wheeler)		UNIX	C++	Maybe
SOAPdenovo	Sequence assembly	Illumina	Linux Mac OS X		Yes	GPLv3
SOAPfusion		Illumina HiSeq Illumina Solexa Illumina	Linux 64	Perl C++	Yes
SOAPsnp				C C++	Yes
SOCS	Read mapping Bisulfite mapping	ABI SOLiD	POSIX	C++	Maybe	GPLv3
Solas				R	Maybe
Sole-Search		Illumina		Java	No
SolexaQA	Sequencing quality control Sequence trimming	Illumina 454	Mac OS X UNIX	Perl R	Yes	GPLv3
SolexaTools	Laboratory information management	Illumina		Java	No
SOLID software tools		ABI SOLiD			Yes	Commercial
SomaticCall					Maybe
Spiral Genetics	Read mapping Sequence alignment File reformatting	Illumina	Linux Mac OS X Windows	C++	Yes	Commercial
SpliceGrapher	Visualisation	Any			Maybe
SpliceMap	Read mapping		Linux	Python C++	Yes
SplicePlot	Visualisation				Maybe
SpliceTrap	Statistical calculation	Illumina	UNIX Linux	C++ Perl	Yes
SplicingViewer	Mapping	Illumina	Linux Windows Mac OS X	Java	Yes	GPL Commercial BioLicense LGPL BSD License
SPLINTER				C C++	Yes	Commercial Freeware
SplitSeek		ABI SOLiD		Perl	Maybe	GPL
SPP	Peak calling	Illumina 454 Sanger SOLiD Ion Torrent		R	Maybe
SR-ASM	Sequence assembly	454	Linux UNIX	C++	Maybe
SRAdb				R	Maybe
SRMA	Localised reassembly	Illumina ABI SOLiD 454		Java C	Yes	GPL
SSA	Sequence analysis Sequence motif comparison Sequence motif discovery		Linux Mac OS X	Fortran F77 C Perl	Yes	GPL
SSAHA	Sequence alignment Local sequence alignment	Sanger 454 Illumina	Linux Mac OS X		Yes	Commercial Freeware
SsahaSNP			Mac OS X Linux 64 Linux Solaris Compaq Alpha		Maybe
SSAKE	Sequence assembly		Linux	Perl	Maybe	GPLv2
SSPACE	Scaffolding	Illumina ABI SOLiD 454	Windows Linux Mac OS X	Perl	Yes
STADEN	Sequence assembly Sequence alignment Visualisation	Sanger 454 Illumina	Linux Windows Mac OS X UNIX	C C++ Tcl Fortran	Yes	BSD
Stampy	Read mapping	Illumina	Linux	Python	Yes	Commercial Freeware
Standalone hamming	Sample Barcoding			Python	Maybe
Standardized Velvet Assembly Report	Visualisation	Any		R Perl	No	GPLv3
STAR	Sequence alignment	Illumina 454 Sanger Ion Torrent PacBio	Linux Unix Mac OS X; x86_64	C++	Yes	GPLv3
Strelka	Variant calling		Linux	Perl	Yes
Subjunc	Read alignment	Illumina HiSeq ABI SOLiD Ion Torrent 454			Yes
Subread	Read mapping	Illumina ABI SOLiD Ion Torrent 454	Linux 64 Mac OS X Mac OS X; x86 64	C	Yes	GPLv3
SuccinctAssembly			Linux		Yes
SUDS genome browser	Genome visualisation			C++	Maybe	GPLv2
Suffixerator	Genome indexing (suffix arrays)		Linux		Maybe
Supersplat	Sequence assembly				Maybe	C++
SUTTA					Maybe	Commercial Freeware
SVDetect				Perl	Maybe
SVMerge		Illumina		Perl	Yes
Swalign	Sequence alignment			C	Maybe	MIT
SWAP454		454			Maybe
SwDMR	Methylation calling	Any	Linux UNIX	Perl R	Yes	GPLv3
Swift	Base-calling		Linux	C++	Maybe	LGPL
SWT					Maybe
SXOligoSearch	Sequence alignment	Illumina			No
Syapse	Visualisation Sequence analysis Differential expression analysis Ontology comparison Exome analysis Variant classification	Any Illumina Ion Torrent Affymetrix Complete Genomics Sanger			Yes
Syzygy				Python R	Yes
T-lex				Perl	Maybe
Ta-si prediction	Phase pattern prediction	Illumina 454	Linux 64 Windows Mac OS X	Java	Yes	Custom Licence
Tablet	Sequence assembly visualisation	Illumina 454 Sanger	Windows OS X Linux	Java	Yes	BSD
TagCleaner	Sequence trimming	Sanger Illumina 454 Ion Torrent PacBio	UNIX Mac OS X Windows		Yes	GPLv3
TagDust	Sequencing quality control	Illumina	Solaris UNIX Linux	C	Yes	GPL
Taipan	Sequence assembly				Maybe
Tally	Sequence contamination filtering Read pre-processing Sequence redundancy removal	Illumina	Linux UNIX Mac OS X	C	Yes	GPLv3
Tallymer	K-mer counting Genome indexing (suffix arrays)		Linux		Maybe
TAPyR	Read mapping	454 Illumina Ion Torrent		C	Yes	GPL
TASE		Illumina		Java	Maybe
TASR	Sequence assembly			Perl	Yes	GPLv2
TEQC	Sequencing quality control			R	Maybe
TileQC	Sequencing quality control			R	Maybe
TiMat2	Genotyping			Java	No	BSD
TMAP	Read mapping	Ion Torrent			Yes
TopHat	Sequence alignment Mapping	Illumina SOLiD 454	Linux Unix	C++	Yes	Boost
TopHat-Fusion					Yes
TOTALRECALLER	Base-calling	Illumina	Linux		Maybe	Commercial Freeware
Tracembler	Sequence assembly		Linux		Maybe
Trans-ABySS					Maybe	BCCA (academic use)
Trimmomatic	File reformatting Sequencing quality control Sequence trimming	Illumina			Maybe
Trinity	Transcriptome assembly	Illumina	Linux	Java C++	Maybe
Tripal	Visualisation			PHP	Yes	Open Source
Tview	Visualisation			C	Yes	BSD MIT
UGENE	Sequence parsing	ABI SOLiD Sanger Illumina 454	Linux Windows Mac OS X	C++	Yes	GPLv3
UnoSeq				Java	Maybe
USeq				Java	Yes	BSD
V-Xtractor	Statistical calculation	Any	UNIX	Perl	Yes	GPL
VAAL	Sequence alignment				Maybe
VAAST	Variant prioritisation	Any			Yes	Commercial Freeware
Variant Effect Predictor	SNP annotation			Perl	Yes
VariantClassifier	SNP annotation				Maybe
Variation toolkit	SNP annotation		Linux	C++	Yes	GPLv3
VariationHunter	Read mapping Variant calling	Illumina	UNIX	C	Yes
VARiD	Statistical calculation	ABI SOLiD Illumina 454 Sanger		C	Yes	GPLv3
VarScan				Java	Yes
VCAKE	Sequence assembly K-mer counting		Linux Mac OS X	Perl C	No	GPL
Vcflib				C++	Yes	MIT
VCFtools				C++	Maybe	GPLv3
Vectorfriends	Sequence assembly Sequence alignment Visualisation Annotation Sequence alignment visualisation	Sanger	Windows	Java	Yes	Free for academic use; Commercial
Velvet	Sequence assembly Sequence assembly (de-novo assembly)	Illumina 454 ABI SOLiD			Yes	GPL
VelvetOptimiser				Perl	Yes	GPLv2
Vicuna		Illumina 454 Ion Torrent	POSIX	C++	Yes
VIP	SNP detection Mapping SNP annotation	454	Linux	Perl MySQL	Maybe	LGPL
ViralFusionSeq	Sequence assembly Read mapping Sequence alignment Read pre-processing	Illumina	Linux	Perl	Yes	GPLv3
VirusHunter					Maybe
VirusSeq	Read mapping	Illumina		Perl	Maybe	Unknown
VisSR	Visualisation	Illumina 454	Linux 64 Windows Mac OS X	Java	Yes	Custom Licence
Vmatch	Read mapping		Linux		Yes	Commercial
WebApollo	Annotation		Requires Tomcat server	JavaScript Perl Java	Yes	Open Source
WebPrInSeS		ABI SOLiD Illumina 454	browser based		Maybe
WHAM	Read mapping	Illumina			Yes	GPLv3
XMatchView	Viewer		Windows Linux	Python	No	GPLv3
YASS					Maybe
ZINBA					Yes	GPLv3
ZOOM	Read mapping		Linux Windows		Maybe
ZORRO	Sequence assembly	Sanger Illumina PacBio 454 Ion Torrent ABI SOLiD	Linux	Perl	Yes	GPL

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