{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,4]],"date-time":"2026-09-04T12:23:34Z","timestamp":1788524614046,"version":"build-2803163510"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2021,7,14]],"date-time":"2021-07-14T00:00:00Z","timestamp":1626220800000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Swiss National Foundation [SNF","award":["205321_184955"],"award-info":[{"award-number":["205321_184955"]}]},{"name":"NCCR Microbiomes","award":["51NF40_180575"],"award-info":[{"award-number":["51NF40_180575"]}]},{"DOI":"10.13039\/501100003006","name":"ETH Z\u00fcrich","doi-asserted-by":"publisher","award":["PHRT-521"],"award-info":[{"award-number":["PHRT-521"]}],"id":[{"id":"10.13039\/501100003006","id-type":"DOI","asserted-by":"publisher"}]},{"name":"BBSRC Institute Strategic Programme Gut Microbes and Health","award":["BB\/r012490\/1"],"award-info":[{"award-number":["BB\/r012490\/1"]}]},{"name":"BBSRC Institute Strategic Programme Gut Microbes and Health","award":["BBS\/e\/F\/000Pr10355"],"award-info":[{"award-number":["BBS\/e\/F\/000Pr10355"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,12,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>\u2002<\/jats:title>\n                  <jats:p>Profiling the taxonomic composition of microbial communities commonly involves the classification of ribosomal RNA gene fragments. As a trade-off to maintain high classification accuracy, existing tools are typically limited to the genus level. Here, we present mTAGs, a taxonomic profiling tool that implements the alignment of metagenomic sequencing reads to degenerate consensus reference sequences of small subunit ribosomal RNA genes. It uses DNA fragments, that is, paired-end sequencing reads, as count units and provides relative abundance profiles at multiple taxonomic ranks, including operational taxonomic units based on a 97% sequence identity cutoff. At the genus rank, mTAGs outperformed other tools across several metrics, such as the F1 score by &amp;gt;11% across data from different environments, and achieved competitive (F1 score) or better results (Bray\u2013Curtis dissimilarity) at the sub-genus level.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The software tool mTAGs is implemented in Python. The source code and binaries are freely available (https:\/\/github.com\/SushiLab\/mTAGs). The data underlying this article are available in Zenodo, at https:\/\/doi.org\/10.5281\/zenodo.4352762.<\/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\/btab465","type":"journal-article","created":{"date-parts":[[2021,7,9]],"date-time":"2021-07-09T19:15:27Z","timestamp":1625858127000},"page":"270-272","source":"Crossref","is-referenced-by-count":27,"title":["mTAGs: taxonomic profiling using degenerate consensus reference sequences of ribosomal RNA genes"],"prefix":"10.1093","volume":"38","author":[{"given":"Guillem","family":"Salazar","sequence":"first","affiliation":[{"name":"Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Z\u00fcrich , 8093 Z\u00fcrich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hans-Joachim","family":"Ruscheweyh","sequence":"additional","affiliation":[{"name":"Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Z\u00fcrich , 8093 Z\u00fcrich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Falk","family":"Hildebrand","sequence":"additional","affiliation":[{"name":"Department of Gut Microbes and Health, Quadram Institute Bioscience, NR4 7UQ Norwich, UK"},{"name":"Department of Digital Biology, Earlham Institute, NR4 7UZ Norwich, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Silvia G","family":"Acinas","sequence":"additional","affiliation":[{"name":"Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC , 08003 Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3065-0314","authenticated-orcid":false,"given":"Shinichi","family":"Sunagawa","sequence":"additional","affiliation":[{"name":"Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Z\u00fcrich , 8093 Z\u00fcrich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,7,13]]},"reference":[{"key":"2023020108384789600_btab465-B1","doi-asserted-by":"crossref","first-page":"8966","DOI":"10.1128\/AEM.71.12.8966-8969.2005","article-title":"PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample","volume":"71","author":"Acinas","year":"2005","journal-title":"Appl. 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