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 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…

• NS
  National Science Foundation

  Awards: DBI-0820619, IOS-1238014, 1238014, 0965342, 0820619
• UD
  U.S. Department of Agriculture
• AR
  Agricultural Research Service