{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,5]],"date-time":"2026-05-05T01:59:58Z","timestamp":1777946398047,"version":"3.51.4"},"reference-count":19,"publisher":"The Open Journal","issue":"121","license":[{"start":{"date-parts":[[2026,5,2]],"date-time":"2026-05-02T00:00:00Z","timestamp":1777680000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,5,2]],"date-time":"2026-05-02T00:00:00Z","timestamp":1777680000000},"content-version":"am","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,5,2]],"date-time":"2026-05-02T00:00:00Z","timestamp":1777680000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["JOSS"],"published-print":{"date-parts":[[2026,5,2]]},"DOI":"10.21105\/joss.09066","type":"journal-article","created":{"date-parts":[[2026,5,2]],"date-time":"2026-05-02T17:08:11Z","timestamp":1777741691000},"page":"9066","source":"Crossref","is-referenced-by-count":0,"title":["YACHT: Software for an ANI-based statistical test to detect microbial presence\/absence in a metagenomic sample"],"prefix":"10.21105","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3440-3919","authenticated-orcid":false,"given":"Maksym","family":"Lupei","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04p491231","id-type":"ROR","asserted-by":"publisher"}],"name":"School of Electrical Engineering and Computer Science, Pennsylvania State University, United States of America"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3112-4068","authenticated-orcid":false,"given":"Shaopeng","family":"Liu","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04p491231","id-type":"ROR","asserted-by":"publisher"}],"name":"Huck Institutes of the Life Sciences, Pennsylvania State University, United States of America"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9731-5153","authenticated-orcid":false,"given":"Chunyu","family":"Ma","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04p491231","id-type":"ROR","asserted-by":"publisher"}],"name":"School of Electrical Engineering and Computer Science, Pennsylvania State University, United States of America"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-4104-2960","authenticated-orcid":false,"given":"Adam","family":"Park","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04p491231","id-type":"ROR","asserted-by":"publisher"}],"name":"School of Electrical Engineering and Computer Science, Pennsylvania State University, United States of America"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-1819-7643","authenticated-orcid":false,"given":"Omar Hesham","family":"Rady","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04p491231","id-type":"ROR","asserted-by":"publisher"}],"name":"School of Electrical Engineering and Computer Science, Pennsylvania State University, United States of America"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5992-9012","authenticated-orcid":false,"given":"Mahmudur Rahman","family":"Hera","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04p491231","id-type":"ROR","asserted-by":"publisher"}],"name":"School of Electrical Engineering and Computer Science, Pennsylvania State University, United States of America"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5109-3054","authenticated-orcid":false,"given":"Judith S.","family":"Rodriguez","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04p491231","id-type":"ROR","asserted-by":"publisher"}],"name":"Huck Institutes of the Life Sciences, Pennsylvania State University, United States of America"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7288-5395","authenticated-orcid":false,"given":"Stephanie J.","family":"Won","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04p491231","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Biology, Pennsylvania State University, United States of America"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0640-954X","authenticated-orcid":false,"given":"David","family":"Koslicki","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04p491231","id-type":"ROR","asserted-by":"publisher"}],"name":"School of Electrical Engineering and Computer Science, Pennsylvania State University, United States of America"},{"id":[{"id":"https:\/\/ror.org\/04p491231","id-type":"ROR","asserted-by":"publisher"}],"name":"Huck Institutes of the Life Sciences, Pennsylvania State University, United States of America"},{"id":[{"id":"https:\/\/ror.org\/04p491231","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Biology, Pennsylvania State University, United States of America"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"8722","reference":[{"issue":"98","key":"irber2024sourmash","doi-asserted-by":"publisher","DOI":"10.21105\/joss.06830","article-title":"Sourmash v4: A multitool to quickly search, compare, and analyze genomic and metagenomic data sets","volume":"9","author":"Irber","year":"2024","unstructured":"Irber, L., Pierce-Ward, N. T., Abuelanin, M., Alexander, H., Anant, A., Barve, K., Baumler, C., Botvinnik, O., Brooks, P., Dsouza, D., & others. (2024). Sourmash v4: A multitool to quickly search, compare, and analyze genomic and metagenomic data sets. Journal of Open Source Software, 9(98), 6830. https:\/\/doi.org\/10.21105\/joss.06830","journal-title":"Journal of Open Source Software"},{"issue":"2","key":"koslicki2024yacht","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btae047","article-title":"YACHT: An ANI-based statistical test to detect microbial presence\/absence in a metagenomic sample","volume":"40","author":"Koslicki","year":"2024","unstructured":"Koslicki, D., White, S., Ma, C., & Novikov, A. (2024). YACHT: An ANI-based statistical test to detect microbial presence\/absence in a metagenomic sample. Bioinformatics, 40(2), btae047. https:\/\/doi.org\/10.1093\/bioinformatics\/btae047","journal-title":"Bioinformatics"},{"issue":"24","key":"ward2018metapoap","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty510","article-title":"MetaPOAP: Presence or absence of metabolic pathways in metagenome-assembled genomes","volume":"34","author":"Ward","year":"2018","unstructured":"Ward, L. M., Shih, P. M., & Fischer, W. W. (2018). MetaPOAP: Presence or absence of metabolic pathways in metagenome-assembled genomes. Bioinformatics, 34(24), 4284\u20134286. https:\/\/doi.org\/10.1093\/bioinformatics\/bty510","journal-title":"Bioinformatics"},{"key":"marcelino2019metatranscriptomics","doi-asserted-by":"publisher","DOI":"10.1186\/s43008-019-0012-8","article-title":"Metatranscriptomics as a tool to identify fungal species and subspecies in mixed communities\u2013a proof of concept under laboratory conditions","volume":"10","author":"Marcelino","year":"2019","unstructured":"Marcelino, V. R., Irinyi, L., Eden, J.-S., Meyer, W., Holmes, E. C., & Sorrell, T. C. (2019). Metatranscriptomics as a tool to identify fungal species and subspecies in mixed communities\u2013a proof of concept under laboratory conditions. IMA Fungus, 10, 1\u201310. https:\/\/doi.org\/10.1186\/s43008-019-0012-8","journal-title":"IMA fungus"},{"issue":"1","key":"pereira2024metatranscriptomics","doi-asserted-by":"publisher","DOI":"10.1080\/19490976.2024.2323235","article-title":"A metatranscriptomics strategy for efficient characterization of the microbiome in human tissues with low microbial biomass","volume":"16","author":"Pereira-Marques","year":"2024","unstructured":"Pereira-Marques, J., Ferreira, R. M., & Figueiredo, C. (2024). A metatranscriptomics strategy for efficient characterization of the microbiome in human tissues with low microbial biomass. Gut Microbes, 16(1), 2323235. https:\/\/doi.org\/10.1080\/19490976.2024.2323235","journal-title":"Gut Microbes"},{"key":"godlewska2020metagenomic","doi-asserted-by":"publisher","DOI":"10.1007\/s00284-020-02163-4","article-title":"Metagenomic studies in inflammatory skin diseases","volume":"77","author":"Godlewska","year":"2020","unstructured":"Godlewska, U., Brzoza, P., Kwiecie\u0144, K., Kwitniewski, M., & Cichy, J. (2020). Metagenomic studies in inflammatory skin diseases. Current Microbiology, 77, 3201\u20133212. https:\/\/doi.org\/10.1007\/s00284-020-02163-4","journal-title":"Current Microbiology"},{"issue":"6","key":"mande2012classification","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbs054","article-title":"Classification of metagenomic sequences: Methods and challenges","volume":"13","author":"Mande","year":"2012","unstructured":"Mande, S. S., Mohammed, M. H., & Ghosh, T. S. (2012). Classification of metagenomic sequences: Methods and challenges. Briefings in Bioinformatics, 13(6), 669\u2013681. https:\/\/doi.org\/10.1093\/bib\/bbs054","journal-title":"Briefings in bioinformatics"},{"issue":"6","key":"shakya2013comparative","doi-asserted-by":"publisher","DOI":"10.1111\/1462-2920.12086","article-title":"Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities","volume":"15","author":"Shakya","year":"2013","unstructured":"Shakya, M., Quince, C., Campbell, J. H., Yang, Z. K., Schadt, C. W., & Podar, M. (2013). Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities. Environmental Microbiology, 15(6), 1882\u20131899. https:\/\/doi.org\/10.1111\/1462-2920.12086","journal-title":"Environmental microbiology"},{"issue":"11","key":"sczyrba2017critical","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4458","article-title":"Critical assessment of metagenome interpretation\u2014a benchmark of metagenomics software","volume":"14","author":"Sczyrba","year":"2017","unstructured":"Sczyrba, A., Hofmann, P., Belmann, P., Koslicki, D., Janssen, S., Dr\u00f6ge, J., Gregor, I., Majda, S., Fiedler, J., Dahms, E., & others. (2017). Critical assessment of metagenome interpretation\u2014a benchmark of metagenomics software. Nature Methods, 14(11), 1063\u20131071. https:\/\/doi.org\/10.1038\/nmeth.4458","journal-title":"Nature methods"},{"issue":"4","key":"meyer2022critical","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-022-01431-4","article-title":"Critical assessment of metagenome interpretation: The second round of challenges","volume":"19","author":"Meyer","year":"2022","unstructured":"Meyer, F., Fritz, A., Deng, Z.-L., Koslicki, D., Lesker, T. R., Gurevich, A., Robertson, G., Alser, M., Antipov, D., Beghini, F., & others. (2022). Critical assessment of metagenome interpretation: The second round of challenges. Nature Methods, 19(4), 429\u2013440. https:\/\/doi.org\/10.1038\/s41592-022-01431-4","journal-title":"Nature methods"},{"key":"schloss2020removal","doi-asserted-by":"publisher","DOI":"10.1101\/2020.12.11.422279","article-title":"Removal of rare amplicon sequence variants from 16S rRNA gene sequence surveys biases the interpretation of community structure data","author":"Schloss","year":"2020","unstructured":"Schloss, P. D. (2020). Removal of rare amplicon sequence variants from 16S rRNA gene sequence surveys biases the interpretation of community structure data. bioRxiv. https:\/\/doi.org\/10.1101\/2020.12.11.422279","journal-title":"bioRxiv"},{"issue":"4","key":"kunin2008bioinformatician","doi-asserted-by":"publisher","DOI":"10.1128\/MMBR.00009-08","article-title":"A bioinformatician\u2019s guide to metagenomics","volume":"72","author":"Kunin","year":"2008","unstructured":"Kunin, V., Copeland, A., Lapidus, A., Mavromatis, K., & Hugenholtz, P. (2008). A bioinformatician\u2019s guide to metagenomics. Microbiology and Molecular Biology Reviews, 72(4), 557\u2013578. https:\/\/doi.org\/10.1128\/MMBR.00009-08","journal-title":"Microbiology and molecular biology reviews"},{"issue":"6","key":"schlaberg2017validation","doi-asserted-by":"publisher","DOI":"10.5858\/arpa.2016-0539-RA","article-title":"Validation of metagenomic next-generation sequencing tests for universal pathogen detection","volume":"141","author":"Schlaberg","year":"2017","unstructured":"Schlaberg, R., Chiu, C. Y., Miller, S., Procop, G. W., Weinstock, G., Professional Practice Committee and Committee on Laboratory Practices of the American Society for Microbiology, & Microbiology Resource Committee of the College of American Pathologists. (2017). Validation of metagenomic next-generation sequencing tests for universal pathogen detection. Archives of Pathology and Laboratory Medicine, 141(6), 776\u2013786. https:\/\/doi.org\/10.5858\/arpa.2016-0539-RA","journal-title":"Archives of Pathology and Laboratory Medicine"},{"key":"loeffler2020improving","doi-asserted-by":"publisher","DOI":"10.1186\/s12915-020-0756-z","article-title":"Improving the usability and comprehensiveness of microbial databases","volume":"18","author":"Loeffler","year":"2020","unstructured":"Loeffler, C., Karlsberg, A., Martin, L. S., Eskin, E., Koslicki, D., & Mangul, S. (2020). Improving the usability and comprehensiveness of microbial databases. BMC Biology, 18, 1\u20136. https:\/\/doi.org\/10.1186\/s12915-020-0756-z","journal-title":"BMC biology"},{"key":"marcelino2020ccmetagen","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-020-02014-2","article-title":"CCMetagen: Comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data","volume":"21","author":"Marcelino","year":"2020","unstructured":"Marcelino, V. R., Clausen, P. T., Buchmann, J. P., Wille, M., Iredell, J. R., Meyer, W., Lund, O., Sorrell, T. C., & Holmes, E. C. (2020). CCMetagen: Comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data. Genome Biology, 21, 1\u201315. https:\/\/doi.org\/10.1186\/s13059-020-02014-2","journal-title":"Genome biology"},{"issue":"1","key":"jia2022sequencing","doi-asserted-by":"publisher","DOI":"10.1186\/s40793-022-00436-y","article-title":"Sequencing introduced false positive rare taxa lead to biased microbial community diversity, assembly, and interaction interpretation in amplicon studies","volume":"17","author":"Jia","year":"2022","unstructured":"Jia, Y., Zhao, S., Guo, W., Peng, L., Zhao, F., Wang, L., Fan, G., Zhu, Y., Xu, D., Liu, G., & others. (2022). Sequencing introduced false positive rare taxa lead to biased microbial community diversity, assembly, and interaction interpretation in amplicon studies. Environmental Microbiome, 17(1), 43. https:\/\/doi.org\/10.1186\/s40793-022-00436-y","journal-title":"Environmental Microbiome"},{"issue":"4","key":"jousset2017less","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2016.174","article-title":"Where less may be more: How the rare biosphere pulls ecosystems strings","volume":"11","author":"Jousset","year":"2017","unstructured":"Jousset, A., Bienhold, C., Chatzinotas, A., Gallien, L., Gobet, A., Kurm, V., K\u00fcsel, K., Rillig, M. C., Rivett, D. W., Salles, J. F., & others. (2017). Where less may be more: How the rare biosphere pulls ecosystems strings. The ISME Journal, 11(4), 853\u2013862. https:\/\/doi.org\/10.1038\/ismej.2016.174","journal-title":"The ISME journal"},{"key":"Irber2022FracMinHash","doi-asserted-by":"publisher","DOI":"10.1101\/2022.01.11.475838","article-title":"Lightweight compositional analysis of metagenomes with FracMinHash and minimum metagenome covers","author":"Irber","year":"2022","unstructured":"Irber, L., Brooks, P. T., Reiter, T. E., Pierce-Ward, N. T., Hera, M. R., Koslicki, D., & Brown, C. T. (2022). Lightweight compositional analysis of metagenomes with FracMinHash and minimum metagenome covers. bioRxiv. https:\/\/doi.org\/10.1101\/2022.01.11.475838","journal-title":"bioRxiv"},{"key":"irber2020decentralizing","volume-title":"Decentralizing indices for genomic data","author":"Irber Jr","year":"2020","unstructured":"Irber Jr, L. C. (2020). Decentralizing indices for genomic data. University of California, Davis."}],"container-title":["Journal of Open Source Software"],"original-title":[],"link":[{"URL":"https:\/\/joss.theoj.org\/papers\/10.21105\/joss.09066.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,5,2]],"date-time":"2026-05-02T17:08:12Z","timestamp":1777741692000},"score":1,"resource":{"primary":{"URL":"https:\/\/joss.theoj.org\/papers\/10.21105\/joss.09066"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,5,2]]},"references-count":19,"journal-issue":{"issue":"121","published-online":{"date-parts":[[2026,5]]}},"alternative-id":["10.21105\/joss.09066"],"URL":"https:\/\/doi.org\/10.21105\/joss.09066","relation":{"has-review":[{"id-type":"uri","id":"https:\/\/github.com\/openjournals\/joss-reviews\/issues\/9066","asserted-by":"subject"}],"references":[{"id-type":"doi","id":"10.5281\/zenodo.19597912","asserted-by":"subject"}]},"ISSN":["2475-9066"],"issn-type":[{"value":"2475-9066","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,5,2]]}}}