High-resolution sweep metagenomics using fast probabilistic inference

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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 ' , Wellcome open research , vol. 5 , no. 14 . https://doi.org/10.12688/wellcomeopenres.15639.2

Title: High-resolution sweep metagenomics using fast probabilistic inference
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
Contributor organization: Department of Mathematics and Statistics
Helsinki Institute for Information Technology
Department of Computer Science
Department of Public Health
Date: 2021-10-08
Language: eng
Number of pages: 28
Belongs to series: Wellcome open research
ISSN: 2398-502X
DOI: https://doi.org/10.12688/wellcomeopenres.15639.2
URI: http://hdl.handle.net/10138/335704
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: 112 Statistics and probability
probabilistic modelling
113 Computer and information sciences
computational biology
laskennallinen biologia
11832 Microbiology and virology
plate sweep
bacterial strain identification
bakteerien tunnistus
Peer reviewed: Yes
Rights: cc_by
Usage restriction: openAccess
Self-archived version: publishedVersion

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