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

摘要: Whole-genome sequencing is a powerful tool for analyzing genetic variation on global scale. One particularly useful application the identification of mutations obtained by classical phenotypic screens in model species. Sequence data from mutant strain aligned to reference genome, and then variants are called generate list candidate alleles. A number software pipelines mutation have been targeted C. elegans, with particular emphasis ease use, incorporation mapping data, subtraction background variants, similar criteria. Although success predicated upon sensitive accurate detection alleles, relatively little effort has invested evaluating underlying components that required identification. Therefore, we benchmarked commonly used tools sequence alignment variant calling, all pair-wise combinations, against both simulated actual datasets. We compared accuracy those found combination BBMap plus FreeBayes calling offers most robust performance.