Fast-GBS

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

Topic

Informatics, Data management, Workflows, Biology, Genetics

Detail

  • 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.

  • Input: -

  • Output: -

  • Contact: -

  • Collection: -

  • Maturity: -

Publications

  • Fast-GBS: a new pipeline for the efficient and highly accurate calling of SNPs from genotyping-by-sequencing data.
  • Torkamaneh D, et al. Fast-GBS: a new pipeline for the efficient and highly accurate calling of SNPs from genotyping-by-sequencing data. Fast-GBS: a new pipeline for the efficient and highly accurate calling of SNPs from genotyping-by-sequencing data. 2017; 18:5. doi: 10.1186/s12859-016-1431-9
  • https://doi.org/10.1186/s12859-016-1431-9
  • PMID: 28049422
  • PMC: PMC5210301
  • Scanning and Filling: Ultra-Dense SNP Genotyping Combining Genotyping-By-Sequencing, SNP Array and Whole-Genome Resequencing Data.
  • Torkamaneh D and Belzile F. Scanning and Filling: Ultra-Dense SNP Genotyping Combining Genotyping-By-Sequencing, SNP Array and Whole-Genome Resequencing Data. Scanning and Filling: Ultra-Dense SNP Genotyping Combining Genotyping-By-Sequencing, SNP Array and Whole-Genome Resequencing Data. 2015; 10:e0131533. doi: 10.1371/journal.pone.0131533
  • https://doi.org/10.1371/journal.pone.0131533
  • PMID: 26161900
  • PMC: PMC4498655
  • Genome-Wide SNP Calling from Genotyping by Sequencing (GBS) Data: A Comparison of Seven Pipelines and Two Sequencing Technologies.
  • Torkamaneh D, et al. Genome-Wide SNP Calling from Genotyping by Sequencing (GBS) Data: A Comparison of Seven Pipelines and Two Sequencing Technologies. Genome-Wide SNP Calling from Genotyping by Sequencing (GBS) Data: A Comparison of Seven Pipelines and Two Sequencing Technologies. 2016; 11:e0161333. doi: 10.1371/journal.pone.0161333
  • https://doi.org/10.1371/journal.pone.0161333
  • PMID: 27547936
  • PMC: PMC4993469

Download and documentation

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