High-resolution sweep metagenomics using fast probabilistic inference [version 2; peer review: 2 approved]

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

Research output: Contribution to journalArticlepeer-review

1 Citation (SciVal)


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.

Original languageEnglish
Article number14
Number of pages20
JournalWellcome Open Research
Early online date30 Jan 2020
Publication statusPublished - 8 Oct 2021


  • bacterial strain identification
  • metagenomics
  • microbial communities
  • plate sweeps
  • probabilistic modeling

ASJC Scopus subject areas

  • Medicine (miscellaneous)
  • Biochemistry, Genetics and Molecular Biology(all)


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