{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:40Z","timestamp":1772138080022,"version":"3.50.1"},"reference-count":3,"publisher":"Oxford University Press (OUP)","issue":"23","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":774,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Motivation: Nanopore sequencing may be the next disruptive technology in genomics, owing to its ability to detect single DNA molecules without prior amplification, lack of reliance on expensive optical components, and the ability to sequence long fragments. The MinION\u2122 from Oxford Nanopore Technologies (ONT) is the first nanopore sequencer to be commercialized and is now available to early-access users. The MinION\u2122 is a USB-connected, portable nanopore sequencer that permits real-time analysis of streaming event data. Currently, the research community lacks a standardized toolkit for the analysis of nanopore datasets.<\/jats:p>\n                  <jats:p>Results: We introduce poretools, a flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION\u2122 for the purposes of quality control and downstream analysis. Poretools operates directly on the native FAST5 (an application of the HDF5 standard) file format produced by ONT and provides a wealth of format conversion utilities and data exploration and visualization tools.<\/jats:p>\n                  <jats:p>Availability and implementation: Poretools is an open-source software and is written in Python as both a suite of command line utilities and a Python application programming interface. Source code is freely available in Github at https:\/\/www.github.com\/arq5x\/poretools<\/jats:p>\n                  <jats:p>Contact: \u00a0n.j.loman@bham.ac.uk and aaronquinlan@gmail.com<\/jats:p>\n                  <jats:p>Supplementary information: An IPython notebook demonstrating the functionality of poretools is in Github. Complete documentation is available at http:\/\/poretools.readthedocs.org.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu555","type":"journal-article","created":{"date-parts":[[2014,8,21]],"date-time":"2014-08-21T00:05:53Z","timestamp":1408579553000},"page":"3399-3401","source":"Crossref","is-referenced-by-count":384,"title":["Poretools: a toolkit for analyzing nanopore sequence data"],"prefix":"10.1093","volume":"30","author":[{"given":"Nicholas J.","family":"Loman","sequence":"first","affiliation":[{"name":"1 Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK and 2Department of Public Health Sciences, University of Virginia, Charlottesville 22932, VA, USA"}]},{"given":"Aaron R.","family":"Quinlan","sequence":"additional","affiliation":[{"name":"1 Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK and 2Department of Public Health Sciences, University of Virginia, Charlottesville 22932, VA, USA"}]}],"member":"286","published-online":{"date-parts":[[2014,8,20]]},"reference":[{"key":"2023012712011559000_btu555-B1","article-title":"Characterization of individual polymer molecules based on monomer-interface interaction","author":"Church","year":"1998"},{"key":"2023012712011559000_btu555-B2","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence alignment\/map (SAM) format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012712011559000_btu555-B3","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/23\/3399\/48931344\/bioinformatics_30_23_3399.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/23\/3399\/48931344\/bioinformatics_30_23_3399.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T07:30:34Z","timestamp":1674804634000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/30\/23\/3399\/207172"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,8,20]]},"references-count":3,"journal-issue":{"issue":"23","published-print":{"date-parts":[[2014,12,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu555","relation":{"has-review":[{"id-type":"doi","id":"10.3410\/f.718541430.793499391","asserted-by":"object"}],"has-preprint":[{"id-type":"doi","id":"10.1101\/007401","asserted-by":"object"}]},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2014,12,1]]},"published":{"date-parts":[[2014,8,20]]}}}