StrainGE

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

van Dijk, L.R. (TU Delft Pattern Recognition and Bioinformatics; Broad Institute of MIT and Harvard)
Walker, Bruce J. (Broad Institute of MIT and Harvard; Applied Invention LLC)
Straub, Timothy J. (Broad Institute of MIT and Harvard; Harvard T.H. Chan School of Public Health)
Worby, Colin J. (Broad Institute of MIT and Harvard)
Grote, Alexandra (Broad Institute of MIT and Harvard)
Schreiber, Henry L. (Washington University School of Medicine)
Anyansi, C.A. (TU Delft Pattern Recognition and Bioinformatics)
Pickering, Amy J. (University of California; Tufts University)
Hultgren, Scott J. (Washington University School of Medicine)
Manson, Abigail L. (Broad Institute of MIT and Harvard)
Abeel, T.E.P.M.F. (TU Delft Pattern Recognition and Bioinformatics; Broad Institute of MIT and Harvard)
Earl, Ashlee M. (Broad Institute of MIT and Harvard)

2022

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.

Metagenomics
Microbiome
Strain-tracking

http://resolver.tudelft.nl/uuid:e0c9a8f9-103e-445c-b007-c93dfae9d8c0

https://doi.org/10.1186/s13059-022-02630-0

1474-7596

Genome Biology (Online), 23 (1)

Institutional Repository

journal article

© 2022 L.R. van Dijk, Bruce J. Walker, Timothy J. Straub, Colin J. Worby, Alexandra Grote, Henry L. Schreiber, C.A. Anyansi, Amy J. Pickering, Scott J. Hultgren, Abigail L. Manson, T.E.P.M.F. Abeel, Ashlee M. Earl