@article{8834d640618f4570a060acdeb6f3ccc0,
title = "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 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.",
keywords = "Assembly graph, Bayesian, Metagenome, Microbial community, Microbiome, Strains",
author = "Christopher Quince and Sergey Nurk and Sebastien Raguideau and Robert James and Soyer, {Orkun S.} and Summers, {J. Kimberly} and Antoine Limasset and Eren, {A. Murat} and Rayan Chikhi and Darling, {Aaron E.}",
note = "Acknowledgements: We thank Tatiana Dvorkina (PhD student in SPbSU) for developing the graph-based codon finding algorithm and fruitful discussions. We also acknowledge constructive criticisms from two anonymous reviewers. Andrew Cosgrove was the primary editor of this article and managed its editorial process and peer review in collaboration with the rest of the editorial team. The review history is available as Additional file 3. Funding Information: This work for made possible through the MRC Methodology Grant {\textquoteleft}Strain resolved metagenomics for medical microbiology{\textquoteright} MR/S037195/1. CQ is also funded through MRC fellowship (MR/M50161X/1) as part of the CLoud Infrastructure for Microbial Genomics (CLIMB) consortium (MR/L015080/1). SR is funded through BBSRC {\textquoteleft}EBI Metagenomics - enabling the reconstruction of microbial populations{\textquoteright} (BB/R015171/1). OSS acknowledges funding through the BBSRC (BB/N023285/1 and BB/L502029/1). This research was supported in part by the Intramural Research Program of the National Human Genome Research Institute, National Institutes of Health (SN). ",
year = "2021",
month = jul,
day = "26",
doi = "10.1186/s13059-021-02419-7",
language = "English",
volume = "22",
journal = "Genome Biology",
issn = "1474-760X",
publisher = "BioMed Central",
}