STRONG: metagenomics strain resolution on assembly graphs

We introduce STrain Resolution ON assembly Graphs (STRONG), which identifies strains de novo, from multiple metagenome samples. STRONG performs coassembly, and binning into metagenome assembled genomes (MAGs), and stores the coassembly graph prior to variant simplification. This enables the subgraph...

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Autores principales: Quince, Christopher, Nurk, Sergey, Raguideau, Sebastien, James, Robert, Soyer, Orkun S., Summers, J. Kimberly, Limasset, Antoine, Eren, A. Murat, Chikhi, Rayan, Darling, Aaron E.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8311964/
https://www.ncbi.nlm.nih.gov/pubmed/34311761
http://dx.doi.org/10.1186/s13059-021-02419-7
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author Quince, Christopher
Nurk, Sergey
Raguideau, Sebastien
James, Robert
Soyer, Orkun S.
Summers, J. Kimberly
Limasset, Antoine
Eren, A. Murat
Chikhi, Rayan
Darling, Aaron E.
author_facet Quince, Christopher
Nurk, Sergey
Raguideau, Sebastien
James, Robert
Soyer, Orkun S.
Summers, J. Kimberly
Limasset, Antoine
Eren, A. Murat
Chikhi, Rayan
Darling, Aaron E.
author_sort Quince, Christopher
collection PubMed
description We introduce STrain Resolution ON assembly Graphs (STRONG), which identifies strains de novo, from multiple metagenome samples. STRONG performs coassembly, and binning into metagenome assembled genomes (MAGs), and stores the coassembly graph prior to variant simplification. This enables the subgraphs and their unitig per-sample coverages, for individual single-copy core genes (SCGs) in each MAG, to be extracted. A Bayesian algorithm, BayesPaths, determines the number of strains present, their haplotypes or sequences on the SCGs, and abundances. STRONG is validated using synthetic communities and for a real anaerobic digestor time series generates haplotypes that match those observed from long Nanopore reads. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at (10.1186/s13059-021-02419-7).
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spelling pubmed-83119642021-07-28 STRONG: metagenomics strain resolution on assembly graphs Quince, Christopher Nurk, Sergey Raguideau, Sebastien James, Robert Soyer, Orkun S. Summers, J. Kimberly Limasset, Antoine Eren, A. Murat Chikhi, Rayan Darling, Aaron E. Genome Biol Method We introduce STrain Resolution ON assembly Graphs (STRONG), which identifies strains de novo, from multiple metagenome samples. STRONG performs coassembly, and binning into metagenome assembled genomes (MAGs), and stores the coassembly graph prior to variant simplification. This enables the subgraphs and their unitig per-sample coverages, for individual single-copy core genes (SCGs) in each MAG, to be extracted. A Bayesian algorithm, BayesPaths, determines the number of strains present, their haplotypes or sequences on the SCGs, and abundances. STRONG is validated using synthetic communities and for a real anaerobic digestor time series generates haplotypes that match those observed from long Nanopore reads. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at (10.1186/s13059-021-02419-7). BioMed Central 2021-07-26 /pmc/articles/PMC8311964/ /pubmed/34311761 http://dx.doi.org/10.1186/s13059-021-02419-7 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Method
Quince, Christopher
Nurk, Sergey
Raguideau, Sebastien
James, Robert
Soyer, Orkun S.
Summers, J. Kimberly
Limasset, Antoine
Eren, A. Murat
Chikhi, Rayan
Darling, Aaron E.
STRONG: metagenomics strain resolution on assembly graphs
title STRONG: metagenomics strain resolution on assembly graphs
title_full STRONG: metagenomics strain resolution on assembly graphs
title_fullStr STRONG: metagenomics strain resolution on assembly graphs
title_full_unstemmed STRONG: metagenomics strain resolution on assembly graphs
title_short STRONG: metagenomics strain resolution on assembly graphs
title_sort strong: metagenomics strain resolution on assembly graphs
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8311964/
https://www.ncbi.nlm.nih.gov/pubmed/34311761
http://dx.doi.org/10.1186/s13059-021-02419-7
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