CoverM: read alignment statistics for metagenomics

Samuel T.N. Aroney; Rhys J.P. Newell; Jakob N. Nissen; Antonio Pedro Camargo; Gene W. Tyson; Ben J. Woodcroft

doi:10.1093/bioinformatics/btaf147

CoverM: read alignment statistics for metagenomics

Samuel T.N. Aroney, Rhys J.P. Newell, Jakob N. Nissen, Antonio Pedro Camargo, Gene W. Tyson, Ben J. Woodcroft^*

^*Corresponding author af dette arbejde

Rasmussen Group

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

2 Citationer (Scopus)

Abstract

Genome-centric analysis of metagenomic samples is a powerful method for understanding the function of microbial communities. Calculating read coverage is a central part of analysis, enabling differential coverage binning for recovery of genomes and estimation of microbial community composition. Coverage is determined by processing read alignments to reference sequences of either contigs or genomes. Per-reference coverage is typically calculated in an ad-hoc manner, with each software package providing its own implementation and specific definition of coverage. Here we present a unified software package CoverM which calculates several coverage statistics for contigs and genomes in an ergonomic and flexible manner. It uses "Mosdepth arrays"for computational efficiency and avoids unnecessary I/O overhead by calculating coverage statistics from streamed read alignment results.

Originalsprog	Engelsk
Artikelnummer	btaf147
Tidsskrift	Bioinformatics
Vol/bind	41
Udgave nummer	4
Antal sider	4
ISSN	1367-4803
DOI	https://doi.org/10.1093/bioinformatics/btaf147
Status	Udgivet - 2025

Bibliografisk note

Publisher Copyright:
© The Author(s) 2025.

Adgang til dokumentet

10.1093/bioinformatics/btaf147Licens: CC BY

FulltextForlagets udgivne version, 1,23 MBLicens: CC BY

Citationsformater

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AU - Aroney, Samuel T.N.

AU - Newell, Rhys J.P.

AU - Nissen, Jakob N.

AU - Camargo, Antonio Pedro

AU - Tyson, Gene W.

AU - Woodcroft, Ben J.

PY - 2025

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AB - Genome-centric analysis of metagenomic samples is a powerful method for understanding the function of microbial communities. Calculating read coverage is a central part of analysis, enabling differential coverage binning for recovery of genomes and estimation of microbial community composition. Coverage is determined by processing read alignments to reference sequences of either contigs or genomes. Per-reference coverage is typically calculated in an ad-hoc manner, with each software package providing its own implementation and specific definition of coverage. Here we present a unified software package CoverM which calculates several coverage statistics for contigs and genomes in an ergonomic and flexible manner. It uses "Mosdepth arrays"for computational efficiency and avoids unnecessary I/O overhead by calculating coverage statistics from streamed read alignment results.

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DO - 10.1093/bioinformatics/btaf147

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SN - 1367-4803

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JO - Bioinformatics

JF - Bioinformatics

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