Phylogenetically typing bacterial strains from partial SNP genotypes observed from direct sequencing of clinical specimen metagenomic data View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2015-06-09

AUTHORS

Jason W. Sahl, James M. Schupp, David A. Rasko, Rebecca E. Colman, Jeffrey T. Foster, Paul Keim

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. More... »

PAGES

52

References to SciGraph publications

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/s13073-015-0176-9

DOI

http://dx.doi.org/10.1186/s13073-015-0176-9

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1032716746

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/26136847


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