GBS-SNP-CROP: a reference-optional pipeline for SNP discovery and plant germplasm characterization using variable length, paired-end genotyping-by-sequencing data

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• 作者：Arthur T. O. Melo ; Radhika Bartaula ; Iago Hale
• 关键词：GBS ; GBS ; SNP ; CROP ; SNP genotyping ; Orphan crops ; Plant genetic resources ; Core collections
• 刊名：BMC Bioinformatics
• 出版年：2016
• 出版时间：December 2016
• 年：2016
• 卷：17
• 期：1
• 全文大小：1,216 KB
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• 作者单位：Arthur T. O. Melo (1)
  Radhika Bartaula (2)
  Iago Hale (1)
  
  1. College of Life Sciences and Agriculture, Department of Biological Sciences, University of New Hampshire, Durham, NH, USA
  2. College of Life Sciences and Agriculture, Genetics Graduate Program, University of New Hampshire, Durham, NH, USA
  
• 刊物主题：Bioinformatics; Microarrays; Computational Biology/Bioinformatics; Computer Appl. in Life Sciences; Combinatorial Libraries; Algorithms;
• 出版者：BioMed Central
• ISSN：1471-2105

文摘

Background With its simple library preparation and robust approach to genome reduction, genotyping-by-sequencing (GBS) is a flexible and cost-effective strategy for SNP discovery and genotyping, provided an appropriate reference genome is available. For resource-limited curation, research, and breeding programs of underutilized plant genetic resources, however, even low-depth references may not be within reach, despite declining sequencing costs. Such programs would find value in an open-source bioinformatics pipeline that can maximize GBS data usage and perform high-density SNP genotyping in the absence of a reference.