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Traditional 16S ribosomal RNA sequencing and whole-genome shotgun metagenomics can determine the composition of bacterial communities on genus level and species level but high-resolution inference on the strain level is challenging due to close relatedness between strain genomes. We present the mSWEEP pipeline for identifying and estimating relative abundances of bacterial strains from plate sweeps of enrichment cultures. mSWEEP uses a database of biologically grouped sequence assemblies as adoi:10.1101/332544 fatcat:f37z34msfvewrpi4a7kttbaqqm