{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:09Z","timestamp":1772138049829,"version":"3.50.1"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2021,12,15]],"date-time":"2021-12-15T00:00:00Z","timestamp":1639526400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"MRFF Investigator","award":["MRF1173594"],"award-info":[{"award-number":["MRF1173594"]}]},{"DOI":"10.13039\/501100022538","name":"The Kinghorn Foundation","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100022538","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,2,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>InterARTIC is an interactive web application for the analysis of viral whole-genome sequencing (WGS) data generated on Oxford Nanopore Technologies (ONT) devices. A graphical interface enables users with no bioinformatics expertise to analyze WGS experiments and reconstruct consensus genome sequences from individual isolates of viruses, such as SARS-CoV-2. InterARTIC is intended to facilitate widespread adoption and standardization of ONT sequencing for viral surveillance and molecular epidemiology.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We demonstrate the use of InterARTIC for the analysis of ONT viral WGS data from SARS-CoV-2 and Ebola virus, using a laptop computer or the internal computer on an ONT GridION sequencing device. We showcase the intuitive graphical interface, workflow customization capabilities and job-scheduling system that facilitate execution of small- and large-scale WGS projects on any common virus.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>InterARTIC is a free, open-source web application implemented in Python that executes best-practice command line workflows from the ARTIC network. The application can be downloaded as a set of pre-compiled binaries that are compatible with all common Linux distributions, Windows with Linux subsystems, MacOSX and ARM systems.\u00a0All code can be found on GitHub at https:\/\/github.com\/Psy-Fer\/interARTIC\/ and documentation can be found at https:\/\/github.com\/Psy-Fer\/interARTIC\/.<\/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\/btab846","type":"journal-article","created":{"date-parts":[[2021,12,12]],"date-time":"2021-12-12T23:06:06Z","timestamp":1639350366000},"page":"1443-1446","source":"Crossref","is-referenced-by-count":11,"title":["InterARTIC: an interactive web application for whole-genome nanopore sequencing analysis of SARS-CoV-2 and other viruses"],"prefix":"10.1093","volume":"38","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 , Sydney, NSW, Australia"}]},{"given":"Hasindu","family":"Gamaarachchi","sequence":"additional","affiliation":[{"name":"Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research , Sydney, NSW, Australia"},{"name":"School of Computer Science and Engineering, University of New South Wales , Sydney, NSW, Australia"}]},{"given":"Thanh","family":"Nguyen","sequence":"additional","affiliation":[{"name":"Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research , Sydney, NSW, Australia"},{"name":"School of Computer Science and Engineering, University of New South Wales , Sydney, NSW, Australia"}]},{"given":"Alyne","family":"Gollon","sequence":"additional","affiliation":[{"name":"Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research , Sydney, NSW, Australia"},{"name":"School of Computer Science and Engineering, University of New South Wales , Sydney, NSW, Australia"}]},{"given":"Stephanie","family":"Tong","sequence":"additional","affiliation":[{"name":"Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research , Sydney, NSW, Australia"},{"name":"School of Computer Science and Engineering, University of New South Wales , Sydney, NSW, Australia"}]},{"given":"Chiara","family":"Aquilina-Reid","sequence":"additional","affiliation":[{"name":"Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research , Sydney, NSW, Australia"},{"name":"School of Computer Science and Engineering, University of New South Wales , Sydney, NSW, Australia"}]},{"given":"Rachel","family":"Bowen-James","sequence":"additional","affiliation":[{"name":"Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research , Sydney, NSW, Australia"},{"name":"School of Computer Science and Engineering, University of New South Wales , Sydney, NSW, Australia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3861-0472","authenticated-orcid":false,"given":"Ira W","family":"Deveson","sequence":"additional","affiliation":[{"name":"Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research , Sydney, NSW, Australia"},{"name":"St Vincent\u2019s Clinical School, Faculty of Medicine, University of New South Wales , Sydney, NSW, Australia"}]}],"member":"286","published-online":{"date-parts":[[2021,12,15]]},"reference":[{"key":"2023020108564995900_btab846-B1","doi-asserted-by":"crossref","first-page":"6272","DOI":"10.1038\/s41467-020-20075-6","article-title":"Analytical validity of nanopore sequencing for rapid SARS-CoV-2 genome analysis","volume":"11","author":"Bull","year":"2020","journal-title":"Nat. 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