{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,4]],"date-time":"2026-06-04T02:13:26Z","timestamp":1780539206970,"version":"3.54.1"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2022,11,2]],"date-time":"2022-11-02T00:00:00Z","timestamp":1667347200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Chan Zuckerberg Biohub, Gladstone Institutes"},{"DOI":"10.13039\/100000050","name":"NHLBI","doi-asserted-by":"publisher","award":["HL160862"],"award-info":[{"award-number":["HL160862"]}],"id":[{"id":"10.13039\/100000050","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"NSF","doi-asserted-by":"publisher","award":["1563159"],"award-info":[{"award-number":["1563159"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>The Metagenomic Intra-Species Diversity Analysis System (MIDAS) is a scalable metagenomic pipeline that identifies single nucleotide variants (SNVs) and gene copy number variants in microbial populations. Here, we present MIDAS2, which addresses the computational challenges presented by increasingly large reference genome databases, while adding functionality for building custom databases and leveraging paired-end reads to improve SNV accuracy. This fast and scalable reengineering of the MIDAS pipeline enables thousands of metagenomic samples to be efficiently genotyped.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The source code is available at https:\/\/github.com\/czbiohub\/MIDAS2.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac713","type":"journal-article","created":{"date-parts":[[2022,10,28]],"date-time":"2022-10-28T17:56:48Z","timestamp":1666979808000},"source":"Crossref","is-referenced-by-count":36,"title":["MIDAS2: Metagenomic Intra-species Diversity Analysis System"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9589-2416","authenticated-orcid":false,"given":"Chunyu","family":"Zhao","sequence":"first","affiliation":[{"name":"Data Science, Chan Zuckerberg Biohub , San Francisco, CA 94158, USA"},{"name":"Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes , San Francisco, CA 94158, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Boris","family":"Dimitrov","sequence":"additional","affiliation":[{"name":"Chan Zuckerberg Initiative , Redwood City, CA 94063, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Miriam","family":"Goldman","sequence":"additional","affiliation":[{"name":"Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes , San Francisco, CA 94158, USA"},{"name":"Biomedical Informatics Graduate Program, University of California San Francisco , San Francisco, CA 94158, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen","family":"Nayfach","sequence":"additional","affiliation":[{"name":"Department of Energy, Joint Genome Institute , Berkeley, CA 94720, USA"},{"name":"Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory , Berkeley, CA 94720, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katherine S","family":"Pollard","sequence":"additional","affiliation":[{"name":"Data Science, Chan Zuckerberg Biohub , San Francisco, CA 94158, USA"},{"name":"Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes , San Francisco, CA 94158, USA"},{"name":"Department of Epidemiology and Biostatistics, University of California , San Francisco, CA 94158, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,11,2]]},"reference":[{"key":"2023022720070019900_","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. 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