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StrainGE: a toolkit to track and characterize low-abundance strains in complex microbial communitiesvan Dijk, L.R. (author), Walker, Bruce J. (author), Straub, Timothy J. (author), Worby, Colin J. (author), Grote, Alexandra (author), Schreiber, Henry L. (author), Anyansi, C.A. (author), Pickering, Amy J. (author), Hultgren, Scott J. (author), Manson, Abigail L. (author), Abeel, T.E.P.M.F. (author), Earl, Ashlee M. (author)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...journal article 2022
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Anyansi, C.A. (author), Keo, D. (author), Walker, Bruce J. (author), Straub, Timothy J. (author), Manson, Abigail L. (author), Earl, Ashlee M. (author), Abeel, T.E.P.M.F. (author)Background: Mixed infections of Mycobacterium tuberculosis and antibiotic heteroresistance continue to complicate tuberculosis (TB) diagnosis and treatment. Detection of mixed infections has been limited to molecular genotyping techniques, which lack the sensitivity and resolution to accurately estimate the multiplicity of TB infections. In...journal article 2020