STRONG: metagenomics strain resolution on assembly graphs
Abstract 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...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2021-07-01
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| Series: | Genome Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13059-021-02419-7 |
| _version_ | 1818885251566403584 |
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| author | Christopher Quince Sergey Nurk Sebastien Raguideau Robert James Orkun S. Soyer J. Kimberly Summers Antoine Limasset A. Murat Eren Rayan Chikhi Aaron E. Darling |
| author_facet | Christopher Quince Sergey Nurk Sebastien Raguideau Robert James Orkun S. Soyer J. Kimberly Summers Antoine Limasset A. Murat Eren Rayan Chikhi Aaron E. Darling |
| author_sort | Christopher Quince |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-12-19T16:02:28Z |
| format | Article |
| id | doaj.art-c74ea889eddf4483a41b363af8e7877a |
| institution | Directory Open Access Journal |
| issn | 1474-760X |
| language | English |
| last_indexed | 2024-12-19T16:02:28Z |
| publishDate | 2021-07-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj.art-c74ea889eddf4483a41b363af8e7877a2022-12-21T20:14:55ZengBMCGenome Biology1474-760X2021-07-0122113410.1186/s13059-021-02419-7STRONG: metagenomics strain resolution on assembly graphsChristopher Quince0Sergey Nurk1Sebastien Raguideau2Robert James3Orkun S. Soyer4J. Kimberly Summers5Antoine Limasset6A. Murat Eren7Rayan Chikhi8Aaron E. Darling9Organisms and Ecosystems, Earlham InstituteGenome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of HealthOrganisms and Ecosystems, Earlham InstituteGut Microbes and Health, Quadram InstituteSchool of Life Sciences, University of WarwickWarwick Medical School, University of WarwickUniv. Lille, CNRS, Inria, UMR 9189 - CRIStALDepartment of Medicine, University of ChicagoDepartment of Computational Biology, Institut Pasteur, C3BI USR 3756 IP CNRSThe iThree institute, University of Technology SydneyAbstract 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.https://doi.org/10.1186/s13059-021-02419-7MicrobiomeMetagenomeStrainsBayesianMicrobial communityAssembly graph |
| spellingShingle | Christopher Quince Sergey Nurk Sebastien Raguideau Robert James Orkun S. Soyer J. Kimberly Summers Antoine Limasset A. Murat Eren Rayan Chikhi Aaron E. Darling STRONG: metagenomics strain resolution on assembly graphs Genome Biology Microbiome Metagenome Strains Bayesian Microbial community Assembly graph |
| 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 | Microbiome Metagenome Strains Bayesian Microbial community Assembly graph |
| url | https://doi.org/10.1186/s13059-021-02419-7 |
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