title: Haplotag: Software for Haplotype-Based Genotyping-by-Sequencing Analysis.
abstract: Genotyping-by-sequencing (GBS), and related methods, are based on high-throughput short-read sequencing of genomic complexity reductions followed by discovery of single nucleotide polymorphisms (SNPs) within sequence tags. This provides a powerful and economical approach to whole-genome genotyping, facilitating applications in genomics, diversity analysis, and molecular breeding. However, due to the complexity of analyzing large data sets, applications of GBS may require substantial time, expertise, and computational resources. Haplotag, the novel GBS software described here, is freely available, and operates with minimal user-investment on widely available computer platforms. Haplotag is unique in fulfilling the following set of criteria: (1) operates without a reference genome; (2) can be used in a polyploid species; (3) provides a discovery mode, and a production mode; (4) discovers polymorphisms based on a model of tag-level haplotypes within sequenced tags; (5) reports SNPs as well as haplotype-based genotypes; and (6) provides an intuitive visual "passport" for each inferred locus. Haplotag is optimized for use in a self-pollinating plant species.
authors.affiliation: Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ontario, K1A 0C6, Canada nick.tinker@canada.ca.
authors.forename: Nicholas A
authors.initials: NA
authors.lastname: Tinker
authors.affiliation: Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ontario, K1A 0C6, Canada.
authors.forename: Wubishet A
authors.initials: WA
authors.lastname: Bekele
authors.affiliation: Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ontario, K1A 0C6, Canada.
authors.forename: Jiro
authors.initials: J
authors.lastname: Hattori
mesh_terms: D019295:Computational Biology / Q000379:methods*; D023281:Genomics / Q000379:methods*; D060005:Genotyping Techniques; D006239:Haplotypes; D020641:Polymorphism, Single Nucleotide; D011123:Polyploidy; D017422:Sequence Analysis, DNA; D012984:Software; D014584:User-Computer Interface; D064878:Web Browser
keywords: genotyping-by-sequencing (GBS); haplotype; pipeline; polyploidy; single nucleotide polymorphism (SNP)
references.citation: PLoS One. 2011;6(5):e19379
references.pmid: 21573248
references.citation: PLoS Genet. 2013;9(1):e1003215
references.pmid: 23349638
references.citation: PLoS One. 2014;9(2):e90346
references.pmid: 24587335
references.citation: PLoS One. 2014;9(7):e102448
references.pmid: 25047601
references.citation: PLoS One. 2010;5(11):e14079
references.pmid: 21124933
references.citation: G3 (Bethesda). 2011 Aug;1(3):171-82
references.pmid: 22384329
references.citation: Genome Res. 2007 Feb;17(2):240-8
references.pmid: 17189378
references.citation: PLoS One. 2013;8(1):e54603
references.pmid: 23372741
references.citation: PLoS One. 2012;7(2):e32253
references.pmid: 22389690