Evaluating alignment and variant-calling software for mutation identification in C. elegans by whole-genome sequencing.

ABSTRACT: Whole-genome sequencing is a powerful tool for analyzing genetic variation on a global scale. One particularly useful application is the identification of mutations obtained by classical phenotypic screens in model species. Sequence data from the mutant strain is aligned to the reference genome, and then variants are called to generate a list of candidate alleles. A number of software pipelines for mutation identification have been targeted to C. elegans, with particular emphasis on ease of use, incorporation of mapping strain data, subtraction of background variants, and similar criteria. Although success is predicated upon the sensitive and accurate detection of candidate alleles, relatively little effort has been invested in evaluating the underlying software components that are require

SUBMITTER: Smith HE 

PROVIDER: S-EPMC5363872 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature