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A pipeline to extract a high-quality SNP catalog. INPUT; FASTQ files obtained from sequencing genotyping-by-sequencing (GBS) libraries.


Informatics, Data management, Workflows, Biology, Genetics


  • Operation: Nucleic acid feature detection, Genetic variation analysis, Polymorphism detection, SNP detection
  • Software interface: Command-line interface
  • Language: Python
  • License: GNU GPL v3
  • Cost: -
  • Version name: -
  • Credit: Torkamaneh D, Laroche J, Bastien M, Abed A, Belzile F.
  • Contact: -
  • Collection: -


Torkamaneh D, Laroche J, Bastien M, Abed A, Belzile F "Fast-GBS: a new pipeline for the efficient and highly accurate calling of SNPs from genotyping-by-sequencing data." BMC Bioinformatics 2017; 18(1):5
PMID: 28049422
PMCID: PMC5210301

Torkamaneh D, Belzile F "Scanning and Filling: Ultra-Dense SNP Genotyping Combining Genotyping-By-Sequencing, SNP Array and Whole-Genome Resequencing Data." PLoS ONE 2015; 10(7):e0131533
PMID: 26161900
PMCID: PMC4498655

Torkamaneh D, Laroche J, Belzile F "Genome-Wide SNP Calling from Genotyping by Sequencing (GBS) Data: A Comparison of Seven Pipelines and Two Sequencing Technologies." PLoS ONE 2016; 11(8):e0161333
PMID: 27547936
PMCID: PMC4993469

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