{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,17]],"date-time":"2026-04-17T20:21:52Z","timestamp":1776457312154,"version":"3.51.2"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"23","license":[{"start":{"date-parts":[[2022,10,11]],"date-time":"2022-10-11T00:00:00Z","timestamp":1665446400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"UQ Strategic Funding and Australian Research Council Laureate Fellowship","award":["FL150100038"],"award-info":[{"award-number":["FL150100038"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,11,30]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>The Genome Taxonomy Database (GTDB) and associated taxonomic classification toolkit (GTDB-Tk) have been widely adopted by the microbiology community. However, the growing size of the GTDB bacterial reference tree has resulted in GTDB-Tk requiring substantial amounts of memory (\u223c320 GB) which limits its adoption and ease of use. Here, we present an update to GTDB-Tk that uses a divide-and-conquer approach where user genomes are initially placed into a bacterial reference tree with family-level representatives followed by placement into an appropriate class-level subtree comprising species representatives. This substantially reduces the memory requirements of GTDB-Tk while having minimal impact on classification.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>GTDB-Tk is implemented in Python and licenced under the GNU General Public Licence v3.0. Source code and documentation are available at: https:\/\/github.com\/ecogenomics\/gtdbtk.<\/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\/btac672","type":"journal-article","created":{"date-parts":[[2022,10,7]],"date-time":"2022-10-07T17:08:19Z","timestamp":1665162499000},"page":"5315-5316","source":"Crossref","is-referenced-by-count":1705,"title":["GTDB-Tk v2: memory friendly classification with the genome taxonomy database"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0426-8445","authenticated-orcid":false,"given":"Pierre-Alain","family":"Chaumeil","sequence":"first","affiliation":[{"name":"Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland , St Lucia, QLD 4072, Australia"},{"name":"Research Computing Center, The University of Queensland , St Lucia, QLD 4072, Australia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9988-0866","authenticated-orcid":false,"given":"Aaron J","family":"Mussig","sequence":"additional","affiliation":[{"name":"Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland , St Lucia, QLD 4072, Australia"}]},{"given":"Philip","family":"Hugenholtz","sequence":"additional","affiliation":[{"name":"Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland , St Lucia, QLD 4072, Australia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6662-9010","authenticated-orcid":false,"given":"Donovan H","family":"Parks","sequence":"additional","affiliation":[{"name":"Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland , St Lucia, QLD 4072, Australia"}]}],"member":"286","published-online":{"date-parts":[[2022,10,11]]},"reference":[{"key":"2022113016193824100_btac672-B1","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":"2022113016193824100_btac672-B2","doi-asserted-by":"crossref","first-page":"1213","DOI":"10.1111\/1755-0998.13527","article-title":"Fast and accurate distance-based phylogenetic placement using divide and conquer","volume":"22","author":"Balaban","year":"2022","journal-title":"Mol. Ecol. Resour"},{"key":"2022113016193824100_btac672-B3","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1093\/sysbio\/syy054","article-title":"EPA-ng: massively parallel evolutionary placement of genetic sequences","volume":"68","author":"Barbera","year":"2019","journal-title":"Syst. Biol"},{"key":"2022113016193824100_btac672-B4","doi-asserted-by":"crossref","first-page":"1925","DOI":"10.1093\/bioinformatics\/btz848","article-title":"GTDB-Tk: a toolkit to classify genomes with the genome taxonomy database","volume":"36","author":"Chaumeil","year":"2019","journal-title":"Bioinformatics"},{"key":"2022113016193824100_btac672-B5","doi-asserted-by":"crossref","first-page":"538","DOI":"10.1186\/1471-2105-11-538","article-title":"Pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree","volume":"11","author":"Matsen","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2022113016193824100_btac672-B6","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1038\/s41587-020-0718-6","article-title":"A genomic catalog of earth\u2019s microbiomes","volume":"39","author":"Nayfach","year":"2021","journal-title":"Nat. Biotechnol"},{"key":"2022113016193824100_btac672-B7","doi-asserted-by":"crossref","first-page":"1079","DOI":"10.1038\/s41587-020-0501-8","article-title":"A complete domain-to-species taxonomy for bacteria and archaea","volume":"38","author":"Parks","year":"2020","journal-title":"Nat. Biotechnol"},{"key":"2022113016193824100_btac672-B8","doi-asserted-by":"crossref","first-page":"D785","DOI":"10.1093\/nar\/gkab776","article-title":"GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy","volume":"50","author":"Parks","year":"2022","journal-title":"Nucleic Acids Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btac672\/46632248\/btac672.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/23\/5315\/47465885\/btac672.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/23\/5315\/47465885\/btac672.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,11,28]],"date-time":"2023-11-28T11:21:18Z","timestamp":1701170478000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/38\/23\/5315\/6758240"}},"subtitle":[],"editor":[{"given":"Karsten","family":"Borgwardt","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2022,10,11]]},"references-count":8,"journal-issue":{"issue":"23","published-online":{"date-parts":[[2022,10,11]]},"published-print":{"date-parts":[[2022,11,30]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btac672","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2022.07.11.499641","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,12,1]]},"published":{"date-parts":[[2022,10,11]]}}}