Expanded functionality, increased accuracy, and enhanced speed in the de novo genotyping-by-sequencing pipeline GBS-SNP-CROP.

ABSTRACT:

Summary

GBS-SNP-CROP is a bioinformatics pipeline originally developed to support the cost-effective genome-wide characterization of plant genetic resources through paired-end genotyping-by-sequencing (GBS), particularly in the absence of a reference genome. Since its 2016 release, the pipeline's functionality has greatly expanded, its computational efficiency has improved, and its applicability to a broad set of genomic studies for both plants and animals has been demonstrated. This note details the suite of improvements to date, as realized in GBS-SNP-CROP v.4.0, with specific attention paid to a new integrated metric that facilitates reliable variant identification despite the complications of homologs. Using the new de novo GBS read simulator GBS-Pacecar, also introduced in thi

SUBMITTER: Melo ATO 

PROVIDER: S-EPMC6513162 | biostudies-literature | 2019 May

REPOSITORIES: biostudies-literature