Table 3: Software applications for NGS analysis.

SoftwareCategoriesSequencing file format compatibilityCreated byOperating platformWeb link

ABySSAssemblyFASTA
FASTQ
QSEQ
SAM
BAM
Jared Simpson et al.
Michael Smith Genome Sciences Centre
Mac OS
Linux
POSIX
http://www.bcgsc.ca/platform/bioinfo/software/abyss/

EdenaAssemblyFASTQDavid Hernandez
University of Geneva Hospitals
Windows
Linux
http://www.genomic.ch/edena.php/

ExonerateAlignmentFASTAGuy Slater and Ewan Birney
European Bioinformatics Institute
Windows
Linux
Unix
http://www.ebi.ac.uk/~guy/exonerate/

MaqAlignmentFASTA
FASTQ
Illumina Bustard & Gerald
Illumina ELAND
Heng LiWindows
Linx
http://maq.sourceforge.net/

MosaikAlignmentFASTA
FASTQ
Illumina Bustard & Gerald
SRF
Michael Stromberg and Gabor Marth
Boston College
Mac OS
Windows
Linux
http://code.google.com/p/mosaik-aligner/

Phrap/
Cross_match/
Swat
AlignmentFASTAPhil Green, Brent Ewing and David Gordon
University of Washington
Mac OS
Windows
Linux
http://www.phrap.org/phredphrapconsed.html

PyroBayesBase CallerSFFAaron Quinlan et al.
Boston College
Linuxhttp://bioinformatics.bc.edu/marthlab/PyroBayes/

SHARCGSAssemblyIllumina Bustard & Gerald
Illumina ELAND
Juliane Dohm et al.
Max Planck Institute
Linuxhttp://sharcgs.molgen.mpg.de/

SHRiMPAlignmentFASTA
FASTQ
SAM
Illumina Bustard & Gerald
Michael Brudno and Stephen Rumble
University of Toronto
Mac OS
Linux
http://compbio.cs.toronto.edu/shrimp/

SOAPAlignment Burrows-WheelerIllumina Bustard & Gerald
Illumina ELAND
Ruiqing Li et al.
Beijing Genomics Institute
Unixhttp://soap.genomics.org.cn/

SSAHA2Alignment Smith-WatermanFASTA
FASTQ
SAM
Illumina Bustard & Gerald
The Wellcome Trust Sanger InstituteMac OS
Linux
http://www.sanger.ac.uk/resources/software/ssaha2/

SSAKEAssemblyFASTARene Warren et al.
Michael Smith Genome Sciences Centre
Linuxhttp://www.bcgsc.ca/platform/bioinfo/software/ssake/

VCAKEAssembly k-mer extensionFASTAWilliam Jeck et al.Mac OS
Linux
http://vcake.sourceforge.net/

VelvetAssemblyFASTA
FASTQ
Illumina Bustard & Gerald
Illumina ELAND
Daniel Zerbino et al.Mac OS
Linux
Cygwin
http://www.ebi.ac.uk/~zerbino/velvet/