{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,21]],"date-time":"2026-04-21T04:24:38Z","timestamp":1776745478216,"version":"3.51.2"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2016,11,16]],"date-time":"2016-11-16T00:00:00Z","timestamp":1479254400000},"content-version":"vor","delay-in-days":67,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>The highly portable Oxford Nanopore MinION sequencer has enabled new applications of genome sequencing directly in the field. However, the MinION currently relies on a cloud computing platform, Metrichor (metrichor.com), for translating locally generated sequencing data into basecalls.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>To allow offline and private analysis of MinION data, we created Nanocall. Nanocall is the first freely available, open-source basecaller for Oxford Nanopore sequencing data and does not require an internet connection. Using R7.3 chemistry, on two E.coli and two human samples, with natural as well as PCR-amplified DNA, Nanocall reads have \u223c68% identity, directly comparable to Metrichor \u20181D\u2019 data. Further, Nanocall is efficient, processing \u223c2500 Kbp of sequence per core hour using the fastest settings, and fully parallelized. Using a 4 core desktop computer, Nanocall could basecall a MinION sequencing run in real time. Metrichor provides the ability to integrate the \u20181D\u2019 sequencing of template and complement strands of a single DNA molecule, and create a \u20182D\u2019 read. Nanocall does not currently integrate this technology, and addition of this capability will be an important future development. In summary, Nanocall is the first open-source, freely available, off-line basecaller for Oxford Nanopore sequencing data.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and Implementation<\/jats:title>\n                    <jats:p>Nanocall is available at github.com\/mateidavid\/nanocall, released under the MIT license.<\/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\/btw569","type":"journal-article","created":{"date-parts":[[2016,9,10]],"date-time":"2016-09-10T20:28:40Z","timestamp":1473539320000},"page":"49-55","source":"Crossref","is-referenced-by-count":110,"title":["Nanocall: an open source basecaller for Oxford Nanopore sequencing data"],"prefix":"10.1093","volume":"33","author":[{"given":"Matei","family":"David","sequence":"first","affiliation":[{"name":"Ontario Institute for Cancer Research, Toronto, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"L J","family":"Dursi","sequence":"additional","affiliation":[{"name":"Ontario Institute for Cancer Research, Toronto, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Delia","family":"Yao","sequence":"additional","affiliation":[{"name":"Ontario Institute for Cancer Research, Toronto, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paul C","family":"Boutros","sequence":"additional","affiliation":[{"name":"Ontario Institute for Cancer Research, Toronto, Canada"},{"name":"Department of Pharmacology and Toxicology, University of Toronto, Toronto, Canada"},{"name":"Department of Medical Biophysics, University of Toronto, Toronto, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jared T","family":"Simpson","sequence":"additional","affiliation":[{"name":"Ontario Institute for Cancer Research, Toronto, Canada"},{"name":"Department of Computer Science, University of Toronto, Toronto, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2016,9,10]]},"reference":[{"key":"2023020204302287500_btw569-B1","first-page":"1","article-title":"An equality and associated maximization technique in statistical estimation for probabilistic functions of Markov processes","volume":"3","author":"Baum","year":"1972","journal-title":"Inequalities"},{"key":"2023020204302287500_btw569-B2","doi-asserted-by":"crossref","DOI":"10.1017\/CBO9780511790492","volume-title":"Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids","author":"Durbin","year":"1998"},{"key":"2023020204302287500_btw569-B3","doi-asserted-by":"crossref","DOI":"10.12688\/f1000research.7201.1","article-title":"Minion analysis and reference consortium: phase 1 data release and analysis","volume":"4","author":"Ip","year":"2015","journal-title":"F1000Research"},{"key":"2023020204302287500_btw569-B4","article-title":"Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM","author":"Li","year":"2013","journal-title":"arXiv Preprint arXiv:1303.3997"},{"key":"2023020204302287500_btw569-B5","doi-asserted-by":"crossref","first-page":"733","DOI":"10.1038\/nmeth.3444","article-title":"A complete bacterial genome assembled de novo using only nanopore sequencing data","volume":"12","author":"Loman","year":"2015","journal-title":"Nat. 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