StrainGE
a toolkit to track and characterize low-abundance strains in complex microbial communities
Lucas R. van Dijk (TU Delft - Pattern Recognition and Bioinformatics, Broad Institute of MIT and Harvard)
Bruce J. Walker (Broad Institute of MIT and Harvard, Applied Invention LLC)
Timothy J. Straub (Harvard T.H. Chan School of Public Health, Broad Institute of MIT and Harvard)
Colin J. Worby (Broad Institute of MIT and Harvard)
Alexandra Grote (Broad Institute of MIT and Harvard)
Henry L. Schreiber (Washington University School of Medicine)
Christine Anyansi (TU Delft - Pattern Recognition and Bioinformatics)
Amy J. Pickering (University of California, Tufts University)
Scott J. Hultgren (Washington University School of Medicine)
Abigail L. Manson (Broad Institute of MIT and Harvard)
Thomas Abeel (TU Delft - Pattern Recognition and Bioinformatics, Broad Institute of MIT and Harvard)
Ashlee M. Earl (Broad Institute of MIT and Harvard)
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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.
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