BiO Tools

Integrated solutions

- CLCbio Genomics Workbench

- Galaxy 

- Genomatix

- JMP Genomics

- NextGENe

- SeqMan Genome Analyser 

- SHORE 

- SlimSearch 

Align/Assemble to a reference

- PerM

- BFAST

- Bowtie

- BWA

- ELAND

- Exonerate

- GenomeMapper 

- GMAP

- gnumap

- MAQ

- MOSAIK

- MrFAST and MrsFAST 

- MUMmer

- Novocraft

- PASS

- RMAP

- SeqMap

- SHRiMP

- Slider

- SOAP

- SSAHA

- SOCS

- SWIFT

- SXOligoSearch

- Vmatch

- Zoom

De novo Align/Assemble

- ABySS

- Edena

- EULER-SR

- MIRA2

- SEQAN

- SHARCGS

- SSAKE

- SOAPdenovo

- VCAKE

- Velvet

- Newbler

SNP/Indel Discovery

- ssahaSNP

- PolyBayesShort

- PyroBayes 

- Crossbow 

Genome Annotation/Genome Browser/Alignment Viewer/Assembly Database

- EagleView 

- LookSeq 

- MapView 

- SAM

- STADEN

- XMatchView

Counting e.g. CHiP-Seq, Bis-Seq, CNV-Seq

- BS-Seq 

- ChiPSeq

- CNV-Seq

- FindPeaks

- MACS

- PeakSeq

- QuEST

- SISSRs

Alternate Base Calling

- Rolexa

- Alta-cyclic

Transcriptomics

- ERANGE

- G-Mo.R-Se

- MapNext

- QPalma

- RSAT 

- Cufflinks

- TopHat