TY - JOUR
AU - 
AB - Next-generation sequencing (NGS) has revolutionized plant and animal research in many ways including new methods of high throughput genotyping. Genotyping-by-sequencing (GBS) has been demonstrated to be a robust and cost-effective genotyping method capable OPEN ACCESS of producing thousands to millions of SNPs across a wide range of species. Undoubtedly, Citation: Torkamaneh D, Laroche J, Belzile F (2016) the greatest barrier to its broader use is the challenge of data analysis. Herein we describe Genome-Wide SNP Calling from Genotyping by Sequencing (GBS) Data: A Comparison of Seven a comprehensive comparison of seven GBS bioinformatics pipelines developed to process Pipelines and Two Sequencing Technologies. PLoS raw GBS sequence data into SNP genotypes. We compared five pipelines requiring a ONE 11(8): e0161333. doi:10.1371/journal. reference genome (TASSEL-GBS v1& v2, Stacks, IGST, and Fast-GBS) and two de novo pone.0161333 pipelines that do not require a reference genome (UNEAK and Stacks). Using Illumina Editor: Hector Candela, Universidad Miguel sequence data from a set of 24 re-sequenced soybean lines, we performed SNP calling Hernández de Elche, SPAIN with these pipelines and compared the GBS SNP calls with the re-sequencing data to Received: January 27, 2016 assess their accuracy. The number of SNPs called without a reference 
TI - Genome-Wide SNP Calling from Genotyping by Sequencing (GBS) Data: A Comparison of Seven Pipelines and Two Sequencing Technologies
JF - PLoS ONE
DO - 10.1371/journal.pone.0161333
DA - 2016-08-22
UR - https://www.deepdyve.com/lp/unpaywall/genome-wide-snp-calling-from-genotyping-by-sequencing-gbs-data-a-5qapC0cc5d
DP - DeepDyve
ER -