{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,26]],"date-time":"2026-06-26T07:03:54Z","timestamp":1782457434011,"version":"3.54.5"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2022,3,24]],"date-time":"2022-03-24T00:00:00Z","timestamp":1648080000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Los Alamos National Laboratory LDRD","award":["20200732ER"],"award-info":[{"award-number":["20200732ER"]}]},{"DOI":"10.13039\/100000774","name":"DTRA","doi-asserted-by":"publisher","award":["CB10152"],"award-info":[{"award-number":["CB10152"]}],"id":[{"id":"10.13039\/100000774","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000774","name":"DTRA","doi-asserted-by":"publisher","award":["CB10623"],"award-info":[{"award-number":["CB10623"]}],"id":[{"id":"10.13039\/100000774","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000015","name":"DOE","doi-asserted-by":"publisher","award":["KP160101"],"award-info":[{"award-number":["KP160101"]}],"id":[{"id":"10.13039\/100000015","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000015","name":"DOE","doi-asserted-by":"publisher","award":["4000150817"],"award-info":[{"award-number":["4000150817"]}],"id":[{"id":"10.13039\/100000015","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Hosting of edge-covid19.edgebioinformatics.orgis provided by the Extreme Science and Engineering Discovery Environment"},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["ACI-1548562"],"award-info":[{"award-number":["ACI-1548562"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["MCB180107"],"award-info":[{"award-number":["MCB180107"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Center for Biotechnology Information of the National Library of Medicine"},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,5,13]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Genomics has become an essential technology for surveilling emerging infectious disease outbreaks. A range of technologies and strategies for pathogen genome enrichment and sequencing are being used by laboratories worldwide, together with different and sometimes ad hoc, analytical procedures for generating genome sequences. A fully integrated analytical process for raw sequence to consensus genome determination, suited to outbreaks such as the ongoing COVID-19 pandemic, is critical to provide a solid genomic basis for epidemiological analyses and well-informed decision making. We have developed a web-based platform and integrated bioinformatic workflows that help to provide consistent high-quality analysis of SARS-CoV-2 sequencing data generated with either the Illumina or Oxford Nanopore Technologies (ONT). Using an intuitive web-based interface, this workflow automates data quality control, SARS-CoV-2 reference-based genome variant and consensus calling, lineage determination and provides the ability to submit the consensus sequence and necessary metadata to GenBank, GISAID and INSDC raw data repositories. We tested workflow usability using real world data and validated the accuracy of variant and lineage analysis using several test datasets, and further performed detailed comparisons with results from the COVID-19 Galaxy Project workflow. Our analyses indicate that EC-19 workflows generate high-quality SARS-CoV-2 genomes. Finally, we share a perspective on patterns and impact observed with Illumina versus ONT technologies on workflow congruence and differences.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>https:\/\/edge-covid19.edgebioinformatics.org, and https:\/\/github.com\/LANL-Bioinformatics\/EDGE\/tree\/SARS-CoV2.<\/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\/btac176","type":"journal-article","created":{"date-parts":[[2022,3,24]],"date-time":"2022-03-24T21:52:41Z","timestamp":1648158761000},"page":"2700-2704","source":"Crossref","is-referenced-by-count":23,"title":["EDGE COVID-19: a web platform to generate submission-ready genomes from SARS-CoV-2 sequencing efforts"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3470-1078","authenticated-orcid":false,"given":"Chien-Chi","family":"Lo","sequence":"first","affiliation":[{"name":"Bioscience Division, Los Alamos National Laboratory , Los Alamos, NM 87545, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3876-691X","authenticated-orcid":false,"given":"Migun","family":"Shakya","sequence":"additional","affiliation":[{"name":"Bioscience Division, Los Alamos National Laboratory , Los Alamos, NM 87545, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ryan","family":"Connor","sequence":"additional","affiliation":[{"name":"National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health , Bethesda, MD 20894, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karen","family":"Davenport","sequence":"additional","affiliation":[{"name":"Bioscience Division, Los Alamos National Laboratory , Los Alamos, NM 87545, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark","family":"Flynn","sequence":"additional","affiliation":[{"name":"Bioscience Division, Los Alamos National Laboratory , Los Alamos, NM 87545, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3457-1632","authenticated-orcid":false,"given":"Ad\u00e1n Myers y","family":"Guti\u00e9rrez","sequence":"additional","affiliation":[{"name":"Bioscience Division, Los Alamos National Laboratory , Los Alamos, NM 87545, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0278-8466","authenticated-orcid":false,"given":"Bin","family":"Hu","sequence":"additional","affiliation":[{"name":"Bioscience Division, Los Alamos National Laboratory , Los Alamos, NM 87545, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Po-E","family":"Li","sequence":"additional","affiliation":[{"name":"Bioscience Division, Los Alamos National Laboratory , Los Alamos, NM 87545, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elais Player","family":"Jackson","sequence":"additional","affiliation":[{"name":"Bioscience Division, Los Alamos National Laboratory , Los Alamos, NM 87545, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yan","family":"Xu","sequence":"additional","affiliation":[{"name":"Bioscience Division, Los Alamos National Laboratory , Los Alamos, NM 87545, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patrick S G","family":"Chain","sequence":"additional","affiliation":[{"name":"Bioscience Division, Los Alamos National Laboratory , Los Alamos, NM 87545, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,3,24]]},"reference":[{"key":"2023020109104753400_btac176-B1","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1186\/s13059-016-0924-1","article-title":"JBrowse: a dynamic web platform for genome visualization and analysis","volume":"17","author":"Buels","year":"2016","journal-title":"Genome Biol"},{"key":"2023020109104753400_btac176-B2","doi-asserted-by":"crossref","first-page":"D67","DOI":"10.1093\/nar\/gkv1276","article-title":"GenBank","volume":"44","author":"Clark","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023020109104753400_btac176-B3","doi-asserted-by":"crossref","first-page":"1326","DOI":"10.1038\/s41467-017-01343-4","article-title":"Mapping and phasing of structural variation in patient genomes using nanopore sequencing","volume":"8","author":"Cretu Stancu","year":"2017","journal-title":"Nat. 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Genet"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btac176\/43293479\/btac176.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/10\/2700\/49010317\/btac176.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/10\/2700\/49010317\/btac176.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T21:04:33Z","timestamp":1675285473000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/38\/10\/2700\/6553662"}},"subtitle":[],"editor":[{"given":"Can","family":"Alkan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2022,3,24]]},"references-count":11,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2022,5,13]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btac176","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,5,15]]},"published":{"date-parts":[[2022,3,24]]}}}