title: Phylogenetically typing bacterial strains from partial SNP genotypes observed from direct sequencing of clinical specimen metagenomic data.
abstract: We describe an approach for genotyping bacterial strains from low coverage genome datasets, including metagenomic data from complex samples. Sequence reads from unknown samples are aligned to a reference genome where the allele states of known SNPs are determined. The Whole Genome Focused Array SNP Typing (WG-FAST) pipeline can identify unknown strains with much less read data than is needed for genome assembly. To test WG-FAST, we resampled SNPs from real samples to understand the relationship between low coverage metagenomic data and accurate phylogenetic placement. WG-FAST can be downloaded from https://github.com/jasonsahl/wgfast.
authors.affiliation: Department of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, AZ USA ; Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011 USA.
authors.forename: Jason W
authors.initials: JW
authors.lastname: Sahl
authors.affiliation: Department of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, AZ USA.
authors.forename: James M
authors.initials: JM
authors.lastname: Schupp
authors.affiliation: Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD USA.
authors.forename: David A
authors.initials: DA
authors.lastname: Rasko
authors.affiliation: Department of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, AZ USA.
authors.forename: Rebecca E
authors.initials: RE
authors.lastname: Colman
authors.affiliation: Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011 USA ; Current address: Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, Durham, NH USA.
authors.forename: Jeffrey T
authors.initials: JT
authors.lastname: Foster
authors.affiliation: Department of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, AZ USA ; Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011 USA.
authors.forename: Paul
authors.initials: P
authors.lastname: Keim