{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,11]],"date-time":"2026-03-11T11:51:27Z","timestamp":1773229887345,"version":"3.50.1"},"reference-count":31,"publisher":"Oxford University Press (OUP)","issue":"Supplement_1","license":[{"start":{"date-parts":[[2024,6,28]],"date-time":"2024-06-28T00:00:00Z","timestamp":1719532800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Advanced Research Computing at Hopkins"},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["OAC 1920103"],"award-info":[{"award-number":["OAC 1920103"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DGE2139757"],"award-info":[{"award-number":["DGE2139757"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000051","name":"National Human Genome Research Institute","doi-asserted-by":"publisher","award":["R01HG011392"],"award-info":[{"award-number":["R01HG011392"]}],"id":[{"id":"10.13039\/100000051","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["IIBR 2029552"],"award-info":[{"award-number":["IIBR 2029552"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U01CA253481"],"award-info":[{"award-number":["U01CA253481"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004412","name":"Human Frontier Science Program","doi-asserted-by":"publisher","award":["RGP0025\/2021"],"award-info":[{"award-number":["RGP0025\/2021"]}],"id":[{"id":"10.13039\/100004412","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,6,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Improvements in nanopore sequencing necessitate efficient classification methods, including pre-filtering and adaptive sampling algorithms that enrich for reads of interest. Signal-based approaches circumvent the computational bottleneck of basecalling. But past methods for signal-based classification do not scale efficiently to large, repetitive references like pangenomes, limiting their utility to partial references or individual genomes. We introduce Sigmoni: a rapid, multiclass classification method based on the r-index that scales to references of hundreds of Gbps. Sigmoni quantizes nanopore signal into a discrete alphabet of picoamp ranges. It performs rapid, approximate matching using matching statistics, classifying reads based on distributions of picoamp matching statistics and co-linearity statistics, all in linear query time without the need for seed-chain-extend. Sigmoni is 10\u2013100\u00d7 faster than previous methods for adaptive sampling in host depletion experiments with improved accuracy, and can query reads against large microbial or human pangenomes. Sigmoni is the first signal-based tool to scale to a complete human genome and pangenome while remaining fast enough for adaptive sampling applications.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Sigmoni is implemented in Python, and is available open-source at https:\/\/github.com\/vshiv18\/sigmoni.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae213","type":"journal-article","created":{"date-parts":[[2024,6,28]],"date-time":"2024-06-28T09:28:13Z","timestamp":1719566893000},"page":"i287-i296","source":"Crossref","is-referenced-by-count":20,"title":["Sigmoni: classification of nanopore signal with a compressed pangenome index"],"prefix":"10.1093","volume":"40","author":[{"given":"Vikram S","family":"Shivakumar","sequence":"first","affiliation":[{"name":"Department of Computer Science, Johns Hopkins University , 3400 North Charles St ., Baltimore, MD 21218, United States"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9933-8508","authenticated-orcid":false,"given":"Omar Y","family":"Ahmed","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Johns Hopkins University , 3400 North Charles St ., Baltimore, MD 21218, United States"}]},{"given":"Sam","family":"Kovaka","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Johns Hopkins University , 3400 North Charles St ., Baltimore, MD 21218, United States"}]},{"given":"Mohsen","family":"Zakeri","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Johns Hopkins University , 3400 North Charles St ., Baltimore, MD 21218, United States"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2437-1976","authenticated-orcid":false,"given":"Ben","family":"Langmead","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Johns Hopkins University , 3400 North Charles St ., Baltimore, MD 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