{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,31]],"date-time":"2026-10-31T13:51:41Z","timestamp":1793454701107,"version":"4.5.0"},"reference-count":26,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2025,4,7]],"date-time":"2025-04-07T00:00:00Z","timestamp":1743984000000},"content-version":"vor","delay-in-days":9,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"EMERGE National Science Foundation","award":["2022070"],"award-info":[{"award-number":["2022070"]}]},{"name":"Genomic Science Program of the United States Department of Energy","award":["DE-SC0004632"],"award-info":[{"award-number":["DE-SC0004632"]}],"id":[{"id":"https:\/\/ror.org\/01bj3aw27","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Genomic Science Program of the United States Department of Energy","award":["DE-SC0010580"],"award-info":[{"award-number":["DE-SC0010580"]}],"id":[{"id":"https:\/\/ror.org\/01bj3aw27","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Genomic Science Program of the United States Department of Energy","award":["DE-SC0016440"],"award-info":[{"award-number":["DE-SC0016440"]}],"id":[{"id":"https:\/\/ror.org\/01bj3aw27","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Genomic Science Program of the United States Department of Energy","award":["DE160100248"],"award-info":[{"award-number":["DE160100248"]}],"id":[{"id":"https:\/\/ror.org\/01bj3aw27","id-type":"ROR","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,3,29]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>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 \u201cMosdepth arrays\u201d for computational efficiency and avoids unnecessary I\/O overhead by calculating coverage statistics from streamed read alignment results.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>CoverM is free software available at https:\/\/github.com\/wwood\/coverm. CoverM is implemented in Rust, with Python (https:\/\/github.com\/apcamargo\/pycoverm) and Julia (https:\/\/github.com\/JuliaBinaryWrappers\/CoverM_jll.jl) interfaces.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf147","type":"journal-article","created":{"date-parts":[[2025,4,7]],"date-time":"2025-04-07T19:58:21Z","timestamp":1744055901000},"source":"Crossref","is-referenced-by-count":599,"title":["CoverM: read alignment statistics for metagenomics"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9806-5846","authenticated-orcid":false,"given":"Samuel T N","family":"Aroney","sequence":"first","affiliation":[{"name":"Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute , Woolloongabba 4102,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rhys J P","family":"Newell","sequence":"additional","affiliation":[{"name":"Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute , Woolloongabba 4102,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2860-7982","authenticated-orcid":false,"given":"Jakob N","family":"Nissen","sequence":"additional","affiliation":[{"name":"The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen , Copenhagen 2200,","place":["Denmark"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Antonio Pedro","family":"Camargo","sequence":"additional","affiliation":[{"name":"Departamento de Gen\u00e9tica e Evolu\u00e7\u00e3o, Instituto de Biologia, Universidade Estadual de Campinas , Campinas, S\u00e3o Paulo 13083-970,","place":["Brazil"]},{"name":"Lawrence Berkeley National Laboratory, DOE Joint Genome Institute , Berkeley, CA 94720,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gene W","family":"Tyson","sequence":"additional","affiliation":[{"name":"Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute , Woolloongabba 4102,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ben J","family":"Woodcroft","sequence":"additional","affiliation":[{"name":"Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute , Woolloongabba 4102,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,4,7]]},"reference":[{"key":"2025041602172799000_btaf147-B1","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1038\/nbt.2579","article-title":"Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes","volume":"31","author":"Albertsen","year":"2013","journal-title":"Nat Biotechnol"},{"key":"2025041602172799000_btaf147-B2","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1038\/s41587-020-0603-3","article-title":"A unified catalog of 204,938 reference genomes from the human gut microbiome","volume":"39","author":"Almeida","year":"2021","journal-title":"Nat Biotechnol"},{"key":"2025041602172799000_btaf147-B3","unstructured":"Aroney STN, Camargo AP, Tyson GW \u00a0et al \u00a0Galah: More scalable dereplication for metagenome assembled genomes. Zenodo \u00a02024. 10.5281\/zenodo.10526086, software: not peer reviewed."},{"key":"2025041602172799000_btaf147-B4","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1186\/s13059-019-1875-0","article-title":"Dashing: fast and accurate genomic distances with HyperLogLog","volume":"20","author":"Baker","year":"2019","journal-title":"Genome Biol"},{"key":"2025041602172799000_btaf147-B5","doi-asserted-by":"crossref","first-page":"giab007","DOI":"10.1093\/gigascience\/giab007","article-title":"HTSlib: C library for reading\/writing high-throughput sequencing data","volume":"10","author":"Bonfield","year":"2021","journal-title":"Gigascience"},{"key":"2025041602172799000_btaf147-B6","doi-asserted-by":"crossref","first-page":"e5882","DOI":"10.7717\/peerj.5882","article-title":"imGLAD: accurate detection and quantification of target organisms in metagenomes","volume":"6","author":"Castro","year":"2018","journal-title":"PeerJ"},{"key":"2025041602172799000_btaf147-B7","doi-asserted-by":"crossref","first-page":"e603","DOI":"10.7717\/peerj.603","article-title":"GroopM: an automated tool for the recovery of population genomes from related metagenomes","volume":"2","author":"Imelfort","year":"2014","journal-title":"PeerJ"},{"key":"2025041602172799000_btaf147-B8","doi-asserted-by":"crossref","first-page":"5114","DOI":"10.1038\/s41467-018-07641-9","article-title":"High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries","volume":"9","author":"Jain","year":"2018","journal-title":"Nat Commun"},{"key":"2025041602172799000_btaf147-B9","doi-asserted-by":"crossref","first-page":"e1165","DOI":"10.7717\/peerj.1165","article-title":"MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities","volume":"3","author":"Kang","year":"2015","journal-title":"PeerJ"},{"key":"2025041602172799000_btaf147-B10","doi-asserted-by":"crossref","first-page":"444","DOI":"10.1093\/bioinformatics\/btv573","article-title":"Rust-Bio: a fast and safe bioinformatics library","volume":"32","author":"K\u00f6ster","year":"2016","journal-title":"Bioinformatics"},{"key":"2025041602172799000_btaf147-B11","author":"Li","year":"2013"},{"key":"2025041602172799000_btaf147-B12","doi-asserted-by":"crossref","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","article-title":"Minimap2: pairwise alignment for nucleotide sequences","volume":"34","author":"Li","year":"2018","journal-title":"Bioinformatics"},{"key":"2025041602172799000_btaf147-B13","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1093\/bioinformatics\/btp692","article-title":"RNA-Seq gene expression estimation with read mapping uncertainty","volume":"26","author":"Li","year":"2010","journal-title":"Bioinformatics"},{"key":"2025041602172799000_btaf147-B14","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1038\/nmeth.1226","article-title":"Mapping and quantifying mammalian transcriptomes by RNA-Seq","volume":"5","author":"Mortazavi","year":"2008","journal-title":"Nat Methods"},{"key":"2025041602172799000_btaf147-B15","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1038\/s41597-022-01392-5","article-title":"The OceanDNA MAG catalog contains over 50,000 prokaryotic genomes originated from various marine environments","volume":"9","author":"Nishimura","year":"2022","journal-title":"Sci. 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