Journal of Pathogens

Review Article

Recent Advances in Molecular Technologies and Their Application in Pathogen Detection in Foods with Particular Reference to Yersinia

Table 3

Software applications for NGS analysis.


Software	Categories	Sequencing file format compatibility	Created by	Operating platform	Web link

ABySS	Assembly	FASTA 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/

Edena	Assembly	FASTQ	David Hernandez University of Geneva Hospitals	Windows Linux	http://www.genomic.ch/edena.php/

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

Maq	Alignment	FASTA FASTQ Illumina Bustard & Gerald Illumina ELAND	Heng Li	Windows Linx	http://maq.sourceforge.net/

Mosaik	Alignment	FASTA 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	Alignment	FASTA	Phil Green, Brent Ewing and David Gordon University of Washington	Mac OS Windows Linux	http://www.phrap.org/phredphrapconsed.html

PyroBayes	Base Caller	SFF	Aaron Quinlan et al. Boston College	Linux	http://bioinformatics.bc.edu/marthlab/PyroBayes/

SHARCGS	Assembly	Illumina Bustard & Gerald Illumina ELAND	Juliane Dohm et al. Max Planck Institute	Linux	http://sharcgs.molgen.mpg.de/

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

SOAP	Alignment Burrows-Wheeler	Illumina Bustard & Gerald Illumina ELAND	Ruiqing Li et al. Beijing Genomics Institute	Unix	http://soap.genomics.org.cn/

SSAHA2	Alignment Smith-Waterman	FASTA FASTQ SAM Illumina Bustard & Gerald	The Wellcome Trust Sanger Institute	Mac OS Linux	http://www.sanger.ac.uk/resources/software/ssaha2/

SSAKE	Assembly	FASTA	Rene Warren et al. Michael Smith Genome Sciences Centre	Linux	http://www.bcgsc.ca/platform/bioinfo/software/ssake/

VCAKE	Assembly k-mer extension	FASTA	William Jeck et al.	Mac OS Linux	http://vcake.sourceforge.net/

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