VariantDetective: an accurate all-in-one pipeline for detecting consensus bacterial SNPs and SVs

Abstract

Abstract Motivation Genomic variations comprise a spectrum of alterations, ranging from single nucleotide polymorphisms (SNPs) to large-scale structural variants (SVs), which play crucial roles in bacterial evolution and species diversification. Accurately identifying SNPs and SVs is beneficial for subsequent evolutionary and epidemiological studies. This study presents VariantDetective (VD), a novel, user-friendly, and all-in-one pipeline combining SNP and SV calling to generate consensus genomic variants using multiple tools. Results The VD pipeline accepts various file types as input to initiate SNP and/or SV calling, and benchmarking results demonstrate VD's robustness and high accuracy across multiple tested datasets when compared to existing variant calling approaches. Availability and implementation The source code, test data, and relevant information for VD are freely accessible at https://github.com/OLF-Bioinformatics/VariantDetective under the MIT License.