StrainGE: a toolkit to track and characterize low-abundance strains in complex microbial communities

Lucas R. van Dijk, Bruce J. Walker, Timothy J. Straub, Colin J. Worby, Alexandra Grote, Henry L. Schreiber, Christine Anyansi, Amy J. Pickering, Scott J. Hultgren, Abigail L. Manson, Thomas Abeel, Ashlee M. Earl

Research output: Contribution to journalArticlepeer-review

3 Scopus citations

Abstract

Human-associated microbial communities comprise not only complex mixtures of bacterial species, but also mixtures of conspecific strains, the implications of which are mostly unknown since strain level dynamics are underexplored due to the difficulties of studying them. We introduce the Strain Genome Explorer (StrainGE) toolkit, which deconvolves strain mixtures and characterizes component strains at the nucleotide level from short-read metagenomic sequencing with higher sensitivity and resolution than other tools. StrainGE is able to identify strains at 0.1x coverage and detect variants for multiple conspecific strains within a sample from coverages as low as 0.5x.

Original languageEnglish
Article number74
JournalGenome biology
Volume23
Issue number1
DOIs
StatePublished - Dec 2022

Keywords

  • Metagenomics
  • Microbiome
  • Strain-tracking

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