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High-resolution sweep metagenomics using fast probabilistic inference

By Tommi Mäklin, Teemu Kallonen, Sophia David, Christine J Boinett, Ben Pascoe, Guillaume Meric, David M. Aanensen, Edward Feil, Stephen Baker, Julian Parkhill, Samuel K Sheppard, Jukka Corander, Antti Honkela

Posted 05 Jun 2018
bioRxiv DOI: 10.1101/332544 (published DOI: 10.12688/wellcomeopenres.15639.1)

Determining the composition of bacterial communities beyond the level of a genus or species is challenging because of the considerable overlap between genomes representing close relatives. Here, we present the mSWEEP method for identifying and estimating the relative abundances of bacterial lineages from plate sweeps of enrichment cultures. mSWEEP leverages biologically grouped sequence assembly databases, applying probabilistic modelling, and provides controls for false positive results. Using sequencing data from major pathogens, we demonstrate significant improvements in lineage quantification and detection accuracy. Our method facilitates investigating cultures comprising mixtures of bacteria, and opens up a new field of plate sweep metagenomics.

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