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Fast-GBS specifications

Information


Unique identifier OMICS_14656
Name Fast-GBS
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data The sequenced DNA fragments from any restriction enzyme-based GBS protocol.
Input format FASTQ
Output data A VCF file containing detailed information on each of the variants, the genotypic data and a log file containing the completed steps of the pipeline.
Output format TXT
Biological technology Illumina
Operating system Unix/Linux
Programming languages Python, Shell (Bash)
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Requirements
sabre, cutadapt, bwa, samtools, platypus, vcf, fastqc
Maintained Yes

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Versioning


No version available

Maintainer


  • person_outline François Belzile

Publication for Fast-GBS

Fast-GBS citations

 (3)
library_books

A comparison of genotyping by sequencing analysis methods on low coverage crop datasets shows advantages of a new workflow, GB eaSy

2017
BMC Bioinformatics
PMCID: 5745977
PMID: 29281959
DOI: 10.1186/s12859-017-2000-6

[…] the Williams 82 soybean reference genome.In terms of SNP yield, the relative ranking of each pipeline remained similar across all three populations: GB-eaSy called the most SNPs, followed in order by Fast-GBS, IGST and Stacks (rank depending on population), and TASSEL-GBS (Fig. ). In Population 1, the number of SNPs identified ranged from 35,328 (TASSEL-GBS) to 88,298 (GB-eaSy). Population 2 had t […]

library_books

Comprehensive description of genomewide nucleotide and structural variation in short‐season soya bean

2017
Plant Biotechnol J
PMCID: 5814582
PMID: 28869792
DOI: 10.1111/pbi.12825

[…] A first panel of 441 accessions (cultivars/advanced breeding lines) were subjected to genotyping‐by‐sequencing (GBS; ApeKI protocol) (Elshire et al., ; Sonah et al., ), and SNPs were called using the Fast‐GBS pipeline (Torkamaneh et al., ). Based on a cladogram produced using these data, a second panel comprising 102 elite accessions (Table ) were selected to capture the diversity among this colle […]

library_books

Genome Wide SNP Calling from Genotyping by Sequencing (GBS) Data: A Comparison of Seven Pipelines and Two Sequencing Technologies

2016
PLoS One
PMCID: 4993469
PMID: 27547936
DOI: 10.1371/journal.pone.0161333

[…] that are polymorphic within a given set of germplasm. The only exception was TASSEL-GBS v1, as, only a quarter of the SNPs present in the resulting catalogue was also present in the set derived using Fast-GBS. This is likely due to the shorter sequences used (only 64 bp) and a large number of “false” SNPs as this pipeline proved the least accurate of all. When using the same pipeline to analyze da […]

Citations

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Fast-GBS institution(s)
Département de Phytologie, Université Laval, Quebec City, QC, Canada; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
Fast-GBS funding source(s)
Supported by Agriculture and AgriFood Canada and the Canadian Field Crop Research Alliance (Grant no. AIP-CL23).

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