High-resolution sweep metagenomics using fast probabilistic inference [version 1; peer review : 1 approved, 1 approved with reservations]

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Mäklin , T , Kallonen , T , David , S , Boinett , C J , Pascoe , B , Méric , G , Aanensen , D M , Feil , E J , Baker , S , Parkhill , J , Sheppard , S K , Corander , J & Honkela , A 2021 , ' High-resolution sweep metagenomics using fast probabilistic inference [version 1; peer review : 1 approved, 1 approved with reservations] ' , Wellcome open research , vol. 5 , no. 14 , pp. 1-20 . https://doi.org/10.12688/WELLCOMEOPENRES.15639.1

Title: High-resolution sweep metagenomics using fast probabilistic inference [version 1; peer review : 1 approved, 1 approved with reservations]
Author: Mäklin, Tommi; Kallonen, Teemu; David, Sophia; Boinett, Christine J.; Pascoe, Ben; Méric, Guillaume; Aanensen, David M.; Feil, Edward J.; Baker, Stephen; Parkhill, Julian; Sheppard, Samuel K.; Corander, Jukka; Honkela, Antti
Other contributor: University of Helsinki, Helsinki Institute for Information Technology HIIT (-2009)
University of Helsinki, University of Helsinki
University of Helsinki, University of Helsinki








Date: 2021
Language: eng
Number of pages: 20
Belongs to series: Wellcome open research
ISSN: 2398-502X
DOI: https://doi.org/10.12688/WELLCOMEOPENRES.15639.1
URI: http://hdl.handle.net/10138/335906
Abstract: 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 pipeline for identifying and estimating the relative sequence 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 pipeline facilitates investigating cultures comprising mixtures of bacteria, and opens up a new field of plate sweep metagenomics.
Subject: bacterial strain identification
metagenomics
microbial communities
plate sweeps
probabilistic modeling
1181 Ecology, evolutionary biology
111 Mathematics
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