{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,5]],"date-time":"2026-01-05T15:17:05Z","timestamp":1767626225209},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2016,10,12]],"date-time":"2016-10-12T00:00:00Z","timestamp":1476230400000},"content-version":"vor","delay-in-days":391,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The Oxford Nanopore MinION sequencer, currently in pre-release testing through the MinION Access Programme (MAP), promises long reads in real-time from an inexpensive, compact, USB device. Tools have been released to extract FASTA\/Q from the MinION base calling output and to provide basic yield statistics. However, no single tool yet exists to provide comprehensive alignment-based quality control and error profile analysis\u2014something that is extremely important given the speed with which the platform is evolving.<\/jats:p>\n               <jats:p>Results: NanoOK generates detailed tabular and graphical output plus an in-depth multi-page PDF report including error profile, quality and yield data. NanoOK is multi-reference, enabling detailed analysis of metagenomic or multiplexed samples. Four popular Nanopore aligners are supported and it is easily extensible to include others.<\/jats:p>\n               <jats:p>Availability and implementation: NanoOK is an open-source software, implemented in Java with supporting R scripts. It has been tested on Linux and Mac OS X and can be downloaded from https:\/\/github.com\/TGAC\/NanoOK. A VirtualBox VM containing all dependencies and the DH10B read set used in this article is available from http:\/\/opendata.tgac.ac.uk\/nanook\/. A Docker image is also available from Docker Hub\u2014see program documentation https:\/\/documentation.tgac.ac.uk\/display\/NANOOK.<\/jats:p>\n               <jats:p>Contact: \u00a0richard.leggett@tgac.ac.uk<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv540","type":"journal-article","created":{"date-parts":[[2015,9,18]],"date-time":"2015-09-18T08:26:51Z","timestamp":1442564811000},"page":"142-144","source":"Crossref","is-referenced-by-count":57,"title":["NanoOK: multi-reference alignment analysis of nanopore sequencing data, quality and error profiles"],"prefix":"10.1093","volume":"32","author":[{"given":"Richard M.","family":"Leggett","sequence":"first","affiliation":[{"name":"The Genome Analysis Centre (TGAC), Norwich NR4 7UH, UK"}]},{"given":"Darren","family":"Heavens","sequence":"additional","affiliation":[{"name":"The Genome Analysis Centre (TGAC), Norwich NR4 7UH, UK"}]},{"given":"Mario","family":"Caccamo","sequence":"additional","affiliation":[{"name":"The Genome Analysis Centre (TGAC), Norwich NR4 7UH, UK"}]},{"given":"Matthew D.","family":"Clark","sequence":"additional","affiliation":[{"name":"The Genome Analysis Centre (TGAC), Norwich NR4 7UH, UK"}]},{"given":"Robert P.","family":"Davey","sequence":"additional","affiliation":[{"name":"The Genome Analysis Centre (TGAC), Norwich NR4 7UH, UK"}]}],"member":"286","published-online":{"date-parts":[[2015,9,17]]},"reference":[{"key":"2023020110201292400_btv540-B1","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1186\/1471-2105-13-238","article-title":"Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory","volume":"13","author":"Chaisson","year":"2012","journal-title":"BMC Bioinformatics"},{"key":"2023020110201292400_btv540-B2","doi-asserted-by":"crossref","first-page":"351","DOI":"10.1038\/nmeth.3290","article-title":"Improved data analysis for the MinION nanopore sequencer","volume":"12","author":"Jain","year":"2015","journal-title":"Nat. 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