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Analyzing rare mutations in metagenomes assembled using long and accurate reads

The advent of long and accurate “HiFi” reads has greatly improved our ability to generate complete metagenome-assembled genomes (MAGs), enabling “complete metagenomics” studies that were nearly impossible to conduct with short reads. In particular, HiFi reads simplify the identification and phasing...

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Detalles Bibliográficos
Autores principales: Fedarko, Marcus W., Kolmogorov, Mikhail, Pevzner, Pavel A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9808630/
https://www.ncbi.nlm.nih.gov/pubmed/36418060
http://dx.doi.org/10.1101/gr.276917.122
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author Fedarko, Marcus W.
Kolmogorov, Mikhail
Pevzner, Pavel A.
author_facet Fedarko, Marcus W.
Kolmogorov, Mikhail
Pevzner, Pavel A.
author_sort Fedarko, Marcus W.
collection PubMed
description The advent of long and accurate “HiFi” reads has greatly improved our ability to generate complete metagenome-assembled genomes (MAGs), enabling “complete metagenomics” studies that were nearly impossible to conduct with short reads. In particular, HiFi reads simplify the identification and phasing of mutations in MAGs: It is increasingly feasible to distinguish between positions that are prone to mutations and positions that rarely ever mutate, and to identify co-occurring groups of mutations. However, the problems of identifying rare mutations in MAGs, estimating the false-discovery rate (FDR) of these identifications, and phasing identified mutations remain open in the context of HiFi data. We present strainFlye, a pipeline for the FDR-controlled identification and analysis of rare mutations in MAGs assembled using HiFi reads. We show that deep HiFi sequencing has the potential to reveal and phase tens of thousands of rare mutations in a single MAG, identify hotspots and coldspots of these mutations, and detail MAGs’ growth dynamics.
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spelling pubmed-98086302023-05-01 Analyzing rare mutations in metagenomes assembled using long and accurate reads Fedarko, Marcus W. Kolmogorov, Mikhail Pevzner, Pavel A. Genome Res Method The advent of long and accurate “HiFi” reads has greatly improved our ability to generate complete metagenome-assembled genomes (MAGs), enabling “complete metagenomics” studies that were nearly impossible to conduct with short reads. In particular, HiFi reads simplify the identification and phasing of mutations in MAGs: It is increasingly feasible to distinguish between positions that are prone to mutations and positions that rarely ever mutate, and to identify co-occurring groups of mutations. However, the problems of identifying rare mutations in MAGs, estimating the false-discovery rate (FDR) of these identifications, and phasing identified mutations remain open in the context of HiFi data. We present strainFlye, a pipeline for the FDR-controlled identification and analysis of rare mutations in MAGs assembled using HiFi reads. We show that deep HiFi sequencing has the potential to reveal and phase tens of thousands of rare mutations in a single MAG, identify hotspots and coldspots of these mutations, and detail MAGs’ growth dynamics. Cold Spring Harbor Laboratory Press 2022 /pmc/articles/PMC9808630/ /pubmed/36418060 http://dx.doi.org/10.1101/gr.276917.122 Text en © 2022 Fedarko et al.; Published by Cold Spring Harbor Laboratory Press https://creativecommons.org/licenses/by-nc/4.0/This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see https://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/ (https://creativecommons.org/licenses/by-nc/4.0/) .
spellingShingle Method
Fedarko, Marcus W.
Kolmogorov, Mikhail
Pevzner, Pavel A.
Analyzing rare mutations in metagenomes assembled using long and accurate reads
title Analyzing rare mutations in metagenomes assembled using long and accurate reads
title_full Analyzing rare mutations in metagenomes assembled using long and accurate reads
title_fullStr Analyzing rare mutations in metagenomes assembled using long and accurate reads
title_full_unstemmed Analyzing rare mutations in metagenomes assembled using long and accurate reads
title_short Analyzing rare mutations in metagenomes assembled using long and accurate reads
title_sort analyzing rare mutations in metagenomes assembled using long and accurate reads
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9808630/
https://www.ncbi.nlm.nih.gov/pubmed/36418060
http://dx.doi.org/10.1101/gr.276917.122
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