{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,11]],"date-time":"2026-03-11T11:51:25Z","timestamp":1773229885868,"version":"3.50.1"},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"Supplement_1","license":[{"start":{"date-parts":[[2021,7,12]],"date-time":"2021-07-12T00:00:00Z","timestamp":1626048000000},"content-version":"vor","delay-in-days":11,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"US National Science Foundation","doi-asserted-by":"crossref","award":["CCF-1816027"],"award-info":[{"award-number":["CCF-1816027"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000051","name":"National Human Genome Research Institute","doi-asserted-by":"publisher","award":["R01HG010040"],"award-info":[{"award-number":["R01HG010040"]}],"id":[{"id":"10.13039\/100000051","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01HG008759"],"award-info":[{"award-number":["R01HG008759"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Department of Biomedical Informatics"},{"DOI":"10.13039\/100017094","name":"Department of Internal Medicine","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100017094","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,8,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Oxford Nanopore Technologies sequencing devices support adaptive sequencing, in which undesired reads can be ejected from a pore in real time. This feature allows targeted sequencing aided by computational methods for mapping partial reads, rather than complex library preparation protocols. However, existing mapping methods either require a computationally expensive base-calling procedure before using aligners to map partial reads or work well only on small genomes.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>In this work, we present a new streaming method that can map nanopore raw signals for real-time selective sequencing. Rather than converting read signals to bases, we propose to convert reference genomes to signals and fully operate in the signal space. Our method features a new way to index reference genomes using k-d trees, a novel seed selection strategy and a seed chaining algorithm tailored toward the current signal characteristics. We implemented the method as a tool Sigmap. Then we evaluated it on both simulated and real data and compared it to the state-of-the-art nanopore raw signal mapper Uncalled. Our results show that Sigmap yields comparable performance on mapping yeast simulated raw signals, and better mapping accuracy on mapping yeast real raw signals with a 4.4\u00d7 speedup. Moreover, our method performed well on mapping raw signals to genomes of size &amp;gt;100 Mbp and correctly mapped 11.49% more real raw signals of green algae, which leads to a significantly higher F1-score (0.9354 versus 0.8660).<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Sigmap code is accessible at https:\/\/github.com\/haowenz\/sigmap.<\/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\/btab264","type":"journal-article","created":{"date-parts":[[2021,5,3]],"date-time":"2021-05-03T19:46:46Z","timestamp":1620071206000},"page":"i477-i483","source":"Crossref","is-referenced-by-count":67,"title":["Real-time mapping of nanopore raw signals"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3513-4573","authenticated-orcid":false,"given":"Haowen","family":"Zhang","sequence":"first","affiliation":[{"name":"School of Computational Science and Engineering, Georgia Institute of Technology , Atlanta, GA, 30332, USA"}]},{"given":"Haoran","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, The Ohio State University , Columbus, OH, 43210, USA"}]},{"given":"Chirag","family":"Jain","sequence":"additional","affiliation":[{"name":"Department of Computational and Data Sciences, Indian Institute of Science , Bangalore KA, 560012, India"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9209-5793","authenticated-orcid":false,"given":"Haoyu","family":"Cheng","sequence":"additional","affiliation":[{"name":"Department of Data Science, Dana-Faber Cancer Institute , Boston, MA, 02215, USA"},{"name":"Department of Biomedical Informatics, Harvard Medical School , Boston, MA, 02215, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9222-4241","authenticated-orcid":false,"given":"Kin Fai","family":"Au","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, The Ohio State University , Columbus, OH, 43210, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4874-2874","authenticated-orcid":false,"given":"Heng","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Data Science, Dana-Faber Cancer Institute , Boston, MA, 02215, USA"},{"name":"Department of Biomedical Informatics, Harvard Medical School , Boston, MA, 02215, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4279-469X","authenticated-orcid":false,"given":"Srinivas","family":"Aluru","sequence":"additional","affiliation":[{"name":"School of Computational Science and Engineering, Georgia Institute of Technology , Atlanta, GA, 30332, USA"},{"name":"Institute for Data Engineering and Science, Georgia Institute of Technology , Atlanta, GA, 30332, USA"}]}],"member":"286","published-online":{"date-parts":[[2021,7,12]]},"reference":[{"key":"2023062410170702900_btab264-B1","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1016\/j.jda.2004.08.011","article-title":"Chaining algorithms for multiple genome comparison","volume":"3","author":"Abouelhoda","year":"2005","journal-title":"J. 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