In Silico Evaluation of Variant Calling Methods for Bacterial Whole-Genome Sequencing Assays.

ABSTRACT: Identification and analysis of clinically relevant strains of bacteria increasingly relies on whole-genome sequencing. The downstream bioinformatics steps necessary for calling variants from short-read sequences are well-established but seldom validated against haploid genomes. We devised an in silico workflow to introduce single nucleotide polymorphisms (SNP) and indels into bacterial reference genomes, and computationally generate sequencing reads based on the mutated genomes. We then applied the method to Mycobacterium tuberculosis H37Rv, Staphylococcus aureus NCTC 8325, and Klebsiella pneumoniae HS11286, and used the synthetic reads as truth sets for evaluating several popular variant callers. Insertions proved especially challenging for most variant callers to correctly identif

SUBMITTER: Seah YM 

PROVIDER: S-EPMC10446864 | biostudies-literature | 2023 Aug

REPOSITORIES: biostudies-literature