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STRONG: metagenomics strain resolution on assembly graphs

by Quince, Christopher , James, Robert , Eren, A. Murat , Chikhi, Rayan , Limasset, Antoine , Nurk, Sergey , Darling, Aaron E. , Raguideau, Sebastien , Soyer, Orkun S. , Summers, J. Kimberly

in Algorithms / Animal Genetics and Genomics / Assembly graph / Bayes Theorem / Bayesian / Bayesian analysis / Bayesian theory / Bioinformatics / Biomedical and Life Sciences / Computer Science / Contig Mapping / Evolutionary Biology / Genes / genome / Genome, Bacterial / Genomes / Haplotypes / Human Genetics / Life Sciences / Metagenome / Metagenomics / Metagenomics - methods / Method / Microbial community / Microbial Consortia - genetics / Microbial Genetics and Genomics / Microbiome / nanopores / Plant Genetics and Genomics / Sequence Analysis, DNA / Software / Strains / time series analysis

2021

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STRONG: metagenomics strain resolution on assembly graphs

by Quince, Christopher , James, Robert , Eren, A. Murat , Chikhi, Rayan , Limasset, Antoine , Nurk, Sergey , Darling, Aaron E. , Raguideau, Sebastien , Soyer, Orkun S. , Summers, J. Kimberly

2021

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STRONG: metagenomics strain resolution on assembly graphs

by Quince, Christopher , James, Robert , Eren, A. Murat , Chikhi, Rayan , Limasset, Antoine , Nurk, Sergey , Darling, Aaron E. , Raguideau, Sebastien , Soyer, Orkun S. , Summers, J. Kimberly

2021

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Journal Article

STRONG: metagenomics strain resolution on assembly graphs

Quince, Christopher,

James, Robert,

Eren, A. Murat,

Chikhi, Rayan,

Limasset, Antoine,

Nurk, Sergey,

Darling, Aaron E.,

Raguideau, Sebastien,

Soyer, Orkun S.,

Summers, J. Kimberly

2021

Overview

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.

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Publisher

BioMed Central,Springer Nature B.V,BMC

Subject

Algorithms

/ Animal Genetics and Genomics