TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline.

Genotyping by sequencing (GBS) is a next generation sequencing based method that takes advantage of reduced representation to enable high throughput genotyping of large numbers of individuals at a large number of SNP markers. The relatively straightforward, robust, and cost-effective GBS protocol is...

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Autores principales:	Jeffrey C Glaubitz, Terry M Casstevens, Fei Lu, James Harriman, Robert J Elshire, Qi Sun, Edward S Buckler
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/739be92435d24707a43ea5ea95adf747
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id	oai:doaj.org-article:739be92435d24707a43ea5ea95adf747
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spelling	oai:doaj.org-article:739be92435d24707a43ea5ea95adf7472021-11-18T08:30:20ZTASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline.1932-620310.1371/journal.pone.0090346https://doaj.org/article/739be92435d24707a43ea5ea95adf7472014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24587335/?tool=EBIhttps://doaj.org/toc/1932-6203Genotyping by sequencing (GBS) is a next generation sequencing based method that takes advantage of reduced representation to enable high throughput genotyping of large numbers of individuals at a large number of SNP markers. The relatively straightforward, robust, and cost-effective GBS protocol is currently being applied in numerous species by a large number of researchers. Herein we describe a bioinformatics pipeline, TASSEL-GBS, designed for the efficient processing of raw GBS sequence data into SNP genotypes. The TASSEL-GBS pipeline successfully fulfills the following key design criteria: (1) Ability to run on the modest computing resources that are typically available to small breeding or ecological research programs, including desktop or laptop machines with only 8-16 GB of RAM, (2) Scalability from small to extremely large studies, where hundreds of thousands or even millions of SNPs can be scored in up to 100,000 individuals (e.g., for large breeding programs or genetic surveys), and (3) Applicability in an accelerated breeding context, requiring rapid turnover from tissue collection to genotypes. Although a reference genome is required, the pipeline can also be run with an unfinished "pseudo-reference" consisting of numerous contigs. We describe the TASSEL-GBS pipeline in detail and benchmark it based upon a large scale, species wide analysis in maize (Zea mays), where the average error rate was reduced to 0.0042 through application of population genetic-based SNP filters. Overall, the GBS assay and the TASSEL-GBS pipeline provide robust tools for studying genomic diversity.Jeffrey C GlaubitzTerry M CasstevensFei LuJames HarrimanRobert J ElshireQi SunEdward S BucklerPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 2, p e90346 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jeffrey C Glaubitz Terry M Casstevens Fei Lu James Harriman Robert J Elshire Qi Sun Edward S Buckler TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline.
description	Genotyping by sequencing (GBS) is a next generation sequencing based method that takes advantage of reduced representation to enable high throughput genotyping of large numbers of individuals at a large number of SNP markers. The relatively straightforward, robust, and cost-effective GBS protocol is currently being applied in numerous species by a large number of researchers. Herein we describe a bioinformatics pipeline, TASSEL-GBS, designed for the efficient processing of raw GBS sequence data into SNP genotypes. The TASSEL-GBS pipeline successfully fulfills the following key design criteria: (1) Ability to run on the modest computing resources that are typically available to small breeding or ecological research programs, including desktop or laptop machines with only 8-16 GB of RAM, (2) Scalability from small to extremely large studies, where hundreds of thousands or even millions of SNPs can be scored in up to 100,000 individuals (e.g., for large breeding programs or genetic surveys), and (3) Applicability in an accelerated breeding context, requiring rapid turnover from tissue collection to genotypes. Although a reference genome is required, the pipeline can also be run with an unfinished "pseudo-reference" consisting of numerous contigs. We describe the TASSEL-GBS pipeline in detail and benchmark it based upon a large scale, species wide analysis in maize (Zea mays), where the average error rate was reduced to 0.0042 through application of population genetic-based SNP filters. Overall, the GBS assay and the TASSEL-GBS pipeline provide robust tools for studying genomic diversity.
format	article
author	Jeffrey C Glaubitz Terry M Casstevens Fei Lu James Harriman Robert J Elshire Qi Sun Edward S Buckler
author_facet	Jeffrey C Glaubitz Terry M Casstevens Fei Lu James Harriman Robert J Elshire Qi Sun Edward S Buckler
author_sort	Jeffrey C Glaubitz
title	TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline.
title_short	TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline.
title_full	TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline.
title_fullStr	TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline.
title_full_unstemmed	TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline.
title_sort	tassel-gbs: a high capacity genotyping by sequencing analysis pipeline.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/739be92435d24707a43ea5ea95adf747
work_keys_str_mv	AT jeffreycglaubitz tasselgbsahighcapacitygenotypingbysequencinganalysispipeline AT terrymcasstevens tasselgbsahighcapacitygenotypingbysequencinganalysispipeline AT feilu tasselgbsahighcapacitygenotypingbysequencinganalysispipeline AT jamesharriman tasselgbsahighcapacitygenotypingbysequencinganalysispipeline AT robertjelshire tasselgbsahighcapacitygenotypingbysequencinganalysispipeline AT qisun tasselgbsahighcapacitygenotypingbysequencinganalysispipeline AT edwardsbuckler tasselgbsahighcapacitygenotypingbysequencinganalysispipeline
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TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline.

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