{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,5]],"date-time":"2026-03-05T15:44:45Z","timestamp":1772725485388,"version":"3.50.1"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2019,7,23]],"date-time":"2019-07-23T00:00:00Z","timestamp":1563840000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100022538","name":"Kinghorn Foundation","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100022538","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Cancer Institute NSW research equipment","award":["REG181268"],"award-info":[{"award-number":["REG181268"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>The management of raw nanopore sequencing data poses a challenge that must be overcome to facilitate the creation of new bioinformatics algorithms predicated on signal analysis. SquiggleKit is a toolkit for manipulating and interrogating nanopore data that simplifies file handling, data extraction, visualization and signal processing.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>SquiggleKit is cross platform and freely available from GitHub at (https:\/\/github.com\/Psy-Fer\/SquiggleKit). Detailed documentation can be found at (https:\/\/psy-fer.github.io\/SquiggleKitDocs\/). All tools have been designed to operate in python 2.7+, with minimal additional libraries.<\/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\/btz586","type":"journal-article","created":{"date-parts":[[2019,7,22]],"date-time":"2019-07-22T07:08:50Z","timestamp":1563779330000},"page":"5372-5373","source":"Crossref","is-referenced-by-count":23,"title":["SquiggleKit: a toolkit for manipulating nanopore signal data"],"prefix":"10.1093","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6192-6937","authenticated-orcid":false,"given":"James M","family":"Ferguson","sequence":"first","affiliation":[{"name":"Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research , Darlinghurst, NSW, Australia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2259-1713","authenticated-orcid":false,"given":"Martin A","family":"Smith","sequence":"additional","affiliation":[{"name":"Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research , Darlinghurst, NSW, Australia"},{"name":"St Vincent's Clinical School , Faculty of Medicine, UNSW Sydney, NSW, Australia"}]}],"member":"286","published-online":{"date-parts":[[2019,7,23]]},"reference":[{"key":"2023013108413671500_btz586-B1","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1038\/nmeth.4577","article-title":"Highly parallel direct RNA sequencing on an array of nanopores","volume":"15","author":"Garalde","year":"2018","journal-title":"Nat. Methods"},{"key":"2023013108413671500_btz586-B2","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1261\/rna.063503.117","article-title":"The RNA modification landscape in human disease","volume":"23","author":"Jonkhout","year":"2017","journal-title":"RNA"},{"key":"2023013108413671500_btz586-B3","doi-asserted-by":"crossref","first-page":"829","DOI":"10.1038\/nbt.2950","article-title":"Decoding long nanopore sequencing reads of natural DNA","volume":"32","author":"Laszlo","year":"2014","journal-title":"Nat. Biotechnol"},{"key":"2023013108413671500_btz586-B4","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1038\/nmeth.4189","article-title":"Mapping DNA methylation with high-throughput nanopore sequencing","volume":"14","author":"Rand","year":"2017","journal-title":"Nat. Methods"},{"key":"2023013108413671500_btz586-B5","doi-asserted-by":"crossref","first-page":"90.","DOI":"10.1186\/s13059-018-1462-9","article-title":"From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy","volume":"19","author":"Rang","year":"2018","journal-title":"Genome Biol"},{"key":"2023013108413671500_btz586-B6","doi-asserted-by":"crossref","first-page":"1897","DOI":"10.1093\/bioinformatics\/btv046","article-title":"Analysis of nanopore data using hidden Markov models","volume":"31","author":"Schreiber","year":"2015","journal-title":"Bioinformatics"},{"key":"2023013108413671500_btz586-B7","doi-asserted-by":"crossref","first-page":"407.","DOI":"10.1038\/nmeth.4184","article-title":"Detecting DNA cytosine methylation using nanopore sequencing","volume":"14","author":"Simpson","year":"2017","journal-title":"Nat. Methods"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btz586\/29173767\/btz586.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/24\/5372\/48978849\/bioinformatics_35_24_5372.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/24\/5372\/48978849\/bioinformatics_35_24_5372.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T13:08:14Z","timestamp":1675170494000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/35\/24\/5372\/5537108"}},"subtitle":[],"editor":[{"given":"Inanc","family":"Birol","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2019,7,23]]},"references-count":7,"journal-issue":{"issue":"24","published-print":{"date-parts":[[2019,12,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btz586","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/549741","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,12,15]]},"published":{"date-parts":[[2019,7,23]]}}}