Details

Autor(en) / Beteiligte

• 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

Titel

High-resolution sweep metagenomics using fast probabilistic inference

Ist Teil von

• Wellcome open research, 2021, Vol.5, p.14

Ort / Verlag

England: Wellcome Trust Limited

Erscheinungsjahr

2021

Link zum Volltext

Quelle

EZB Electronic Journals Library

Beschreibungen/Notizen

• 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.