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. Author manuscript; available in PMC: 2011 Apr 13.
Published in final edited form as: J Genet Genomics. 2011 Mar 15;38(3):95–109. doi: 10.1016/j.jgg.2011.02.003

Table 3.

The alignment, assembly and utility bioinformatic tools for NGS.

Program Function Platform Website
De novo assembly
Abyss Alignment/assembly Illumina http://www.bcgsc.ca/platform/bioinfo/software/abyss
ALLPATHS Alignment/assembly Illumina http://www.broadinstitute.org/science/programs/genome-biology/crd
AMOScmp Alignment/assembly Roche http://sourceforge.net/projects/amos/files/
ARACHNE Alignment/assembly Roche http://www.broadinstitute.org/science/programs/genome-biology/crd
CAP3 Alignment/assembly Roche http://pbil.univ-lyon1.fr/cap3.php
consensus/Seq-Cons Alignment/assembly Roche http://www.seqan.de/downloads/projects.html
Curtain Alignment/assembly Illumina/Roche/ABI http://code.google.com/p/curtain/
Edena Alignment/assembly Illumina http://www.genomic.ch/edena
Euler-SR Alignment/assembly Illumina/Roche http://euler-assembler.ucsd.edu/portal/?q=team
FuzzyPath Alignment/assembly Illumina/Roche ftp://ftp.sanger.ac.uk/pub/zn1/fuzzypath/fuzzypath_v3.0.tgz
IDBA Alignment/assembly Illumina http://www.cs.hku.hk/~alse/idba/
MIRA/MIRA3 Alignment/assembly Illumina/Roche http://chevreux.org/projects_mira.html
Newbler Alignment/assembly Roche roche-applied-science.com/
Phrap Alignment/assembly Illumina/Roche http://www.phrap.org/consed/consed.html#howToGet
RGA Alignment/assembly Illumina http://rga.cgrb.oregonstate.edu/
QSRA Alignment/assembly Illumina http://qsra.cgrb.oregonstate.edu/
SHARCGS Alignment/assembly Illumina http://sharcgs.molgen.mpg.de/
SHORTY Alignment/assembly ABI http://www.cs.sunysb.edu/~skiena/shorty/
SHRAP Alignment/assembly Roche By request
SOAPdenovo Alignment/assembly Illumina http://soap.genomics.org.cn
SOPRA Alignment/assembly Illumina/ABI http://www.physics.rutgers.edu/%7Eanirvans/SOPRA/
SR-ASM Alignment/assembly Roche http://bioserver.cs.put.poznan.pl/sr-asm-short-reads-assembly-algorithm
SSAKE Alignment/assembly Illumina/Roche http://www.bcgsc.ca/platform/bioinfo/software/ssake
Taipan Alignment/assembly Illumina http://sourceforge.net/projects/taipan/files/
VCAKE Alignment/assembly Illumina/Roche http://sourceforge.net/projects/vcake
Velvet Alignment/assembly Illumina/Roche/ABI http://www.ebi.ac.uk/%7Ezerbino/velvet
Reference-based assembly
BFAST Alignment/assembly Illumina/ABI http://sourceforge.net/apps/mediawiki/bfast/index.php?title=Main_Page
Bowtie Alignment/assembly Illumina/Roche/ABI http://bowtie-bio.sourceforge.net
BWA Alignment/assembly Illumina/ABI http://bio-bwa.sourceforge.net/bwa.shtml
CoronaLite Alignment/assembly ABI http://solidsoftwaretools.com/gf/project/corona/
CABOG Alignment/assembly Roche/ABI http://wgs-assembler.sf.net
ELAND/ELAND2 Alignment/assembly Illumina/ABI http://www.illumina.com/
EULER Alignment/assembly Illumina http://euler-assembler.ucsd.edu/portal/
Exonerate Alignment/assembly Roche http://www.ebi.ac.uk/~guy/exonerate
EMBF Alignment/assembly Illumina http://www.biomedcentral.com/1471-2105/10?issue=S1
GenomeMapper Alignment/assembly Illumina http://1001genomes.org/downloads/genomemapper.html
GMAP Alignment/assembly Illumina http://www.gene.com/share/gmap
gnumap Alignment/assembly Illumina http://dna.cs.byu.edu/gnumap/
ICON Alignment/assembly Illumina http://icorn.sourceforge.net/
Karma Alignment/assembly Illumina/ABI http://www.sph.umich.edu/csg/pha/karma/
LAST Alignment/assembly Illumina http://last.cbrc.jp/
LOCAS Alignment/assembly Illumina http://www-ab.informatik.uni-tuebingen.de/software/locas
Mapreads Alignment/assembly ABI http://solidsoftwaretools.com/gf/project/mapreads/
MAQ Alignment/assembly Illumina/ABI http://maq.sourceforge.net
MOM Alignment/assembly Illumina http://mom.csbc.vcu.edu/
Mosaik Alignment/assembly Illumina/Roche/ABI http://bioinformatics.bc.edu/marthlab/Mosaik
mrFAST/mrsFAST Alignment/assembly Illumina http://mrfast.sourceforge.net/
MUMer Alignment/assembly ABI http://mummer.sourceforge.net/
nexalign Alignment/assembly Illumina http://genome.gsc.riken.jp/osc/english/dataresource/
Novocraft Alignment/assembly Illumina http://www.novocraft.com/
PerM Alignment/assembly Illumina/ABI http://code.google.com/p/perm/
RazerS Alignment/assembly Illumina/ABI http://www.seqan.de/projects/razers.html
RMAP Alignment/assembly Illumina http://rulai.cshl.edu/rmap
segemehl Alignment/assembly Illumina/Roche http://www.bioinf.uni-leipzig.de/Software/segemehl/
SeqCons Alignment/assembly Roche http://www.seqan.de/projects/seqcons.html
SeqMap Alignment/assembly Illumina http://biogibbs.stanford.edu/*jiangh/SeqMap/
SHRiMP Alignment/assembly Illumina/Roche/ABI http://compbio.cs.toronto.edu/shrimp
Slider/SliderII Alignment/assembly Illumina http://www.bcgsc.ca/platform/bioinfo/software/slider
SOCS Alignment/assembly ABI http://solidsoftwaretools.com/gf/project/socs/
SOAP/SOAP2 Alignment/assembly Illumina/ABI http://soap.genomics.org.cn
SSAHA/SSAHA2 Alignment/assembly Illumina/Roche http://www.sanger.ac.uk/Software/analysis/SSAHA2
Stampy Alignment/assembly Illumina http://www.well.ox.ac.uk/~marting/
SXOligoSearch Alignment/assembly Illumina http://synasite.mgrc.com.my:8080/sxog/NewSXOligoSearch.php
SHORE Alignment/assembly Illumina http://1001genomes.org/downloads/shore.html
Vmatch Alignment/assembly Illumina http://www.vmatch.de/
Diagnostics/utilities
Artemis/ACT Visualization tool Illumina/Roche http://www.sanger.ac.uk/resources/software/artemis/
CASHX Pipeline Illumina http://seqanswers.com/wiki/CASHX
Consed Visualization tool Illumina/Roche http://www.genome.washington.edu/consed/consed.html
EagleView Visualization tool Illumina/Roche http://bioinformatics.bc.edu/marthlab/EagleView
FastQC Quality assessment Illumina/ABI http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/
Gambit Visualization tool Illumina/Roche http://bioinformatics.bc.edu/marthlab/Gambit
Goby Data management Illumina/Roche/ABI http://campagnelab.org/software/goby/
G-SQZ Data management Illumina/ABI http://public.tgen.org/sqz
Hawkeye Visualization tool Illumina/Roche http://amos.sourceforge.net/hawkeye
Hybrid-SHREC Error Correction Illumina/Roche/ABI http://www.cs.helsinki.fi/u/lmsalmel/hybrid-shrec/
IGV Visualization tool Illumina http://www.broadinstitute.org/igv/?q=home
LookSeq Visualization tool Illumina/Roche http://lookseq.sourceforge.net
MagicViewer Visualization tool Illumina http://bioinformatics.zj.cn/magicviewer/
MapView Visualization tool Illumina http://evolution.sysu.edu.cn/mapview/
NGSView Visualization tool Illumina/ABI http://ngsview.sourceforge.net
PIQA Quality assessment Illumina http://bioinfo.uh.edu/PIQA
Reconciliation Assembly pipeline Illumina http://www.genome.umd.edu/software.htm
RefCov Sequence coverage Illumina/Roche http://genome.wustl.edu/tools/cancer-genomics
SAM Tools Utilities Illumina/Roche http://sourceforge.net/projects/samtools/files/
Savant Visualization tool Illumina/Roche http://compbio.cs.toronto.edu/savant/
ShortRead Quality assessment Illumina/Roche http://bioconductor.org/packages/2.6/bioc/html/ShortRead.html
SHREC Error Correction Illumina/Roche http://www.informatik.uni-kiel.de/jasc/Shrec/
Staden Tools (GAP5) Pipeline Illumina/Roche http://sourceforge.net/projects/staden/files/
Tablet Visualization tool Illumina/Roche http://bioinf.scri.ac.uk/tablet
TagDust Data cleaning Illumina http://genome.gsc.riken.jp/osc/english/software/.
TileQC Quality assessment Illumina http://www.science.oregonstate.edu/~dolanp/tileqc
XMatchView Visualization tool Illumina/Roche http://www.bcgsc.ca/platform/bioinfo/software/xmatchview
Yenta Visualization tool Illumina http://genome.wustl.edu/tools/cancer-genomics
Geneus Data management Illumina/ABI http://www.genologics.com/solutions/research-informatics/