mStrain: strain-level identification of Yersinia pestis using metagenomic data

Motivation High-resolution target pathogen detection using metagenomic sequencing data represents a major challenge due to the low concentration of target pathogens in samples. We introduced mStrain, a novel Yesinia pestis strain/lineage-level identification tool that utilizes metagenomic data. mStrain successfully identified Y. pestis at the strain/lineage level by extracting sufficient information regarding single-nucleotide polymorphisms (SNPs), which can therefore be an effective tool for identification and source tracking of Y. pestis based on metagenomic data during a plague outbreak.Strain-level identification Assigning the reads in the metagenomic sequencing data to an exactly known or most closely representative Y. pestis strain.Lineage-level identification Assigning the reads in the metagenomic sequencing data to a specific lineage on the phylogenetic tree.canoSNPs The unique and typical SNPs present in all representative strains.Ancestor/derived state An SNP is defined as the ancestor state when consistent with the allele of Yersinia pseudotuberculosis strain IP32953; otherwise, the SNP is defined as the derived state.Availability and implementation The code for running mStrain, the test dataset, and instructions for running the code can be found at the following GitHub repository: https://github.com/xwqian1123/mStrain.