PT - JOURNAL ARTICLE AU - Nicholas A. Tinker AU - Wubishet A. Bekele AU - Jiro Hattori TI - Haplotag: software for haplotype-based genotyping-by-sequencing analysis AID - 10.1101/031013 DP - 2015 Jan 01 TA - bioRxiv PG - 031013 4099 - http://biorxiv.org/content/early/2015/11/09/031013.short 4100 - http://biorxiv.org/content/early/2015/11/09/031013.full AB - Genotyping-by-sequencing (GBS) and related methods are based on high-throughput short-read sequencing of genomic complexity reductions followed by discovery of 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 analysing 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 local haplotypes within sequenced tags; (5) reports SNPs as well as haplotype-based genotypes; (6) provides an intuitive visual “passport” for each inferred locus.Summary This report describes and makes freely available a novel software application designed to analyze and report results of genotyping-by-sequencing. The software takes a novel approach to discovery and validation of loci based on local haplotypes within sequenced tags. Output from these analysis are formatted as intuitive passports for each cluster of orthologous loci.