{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,7]],"date-time":"2025-11-07T19:02:14Z","timestamp":1762542134995},"reference-count":4,"publisher":"Oxford University Press (OUP)","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Velvet is a popular open-source de novo genome assembly software tool, which is run from the Unix command line. Most of the problems experienced by new users of Velvet revolve around constructing syntactically and semantically correct command lines, getting input files into acceptable formats and assessing the output. Here, we present Velvet Assembler Graphical User Environment (VAGUE), a multi-platform graphical front-end for Velvet. VAGUE aims to make sequence assembly accessible to a wider audience and to facilitate better usage amongst existing users of Velvet.<\/jats:p>\n               <jats:p>Availability and implementation: VAGUE is implemented in JRuby and targets the Java Virtual Machine. It is available under an open-source GPLv2 licence from http:\/\/www.vicbioinformatics.com\/.<\/jats:p>\n               <jats:p>Contact: \u00a0torsten.seemann@monash.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts664","type":"journal-article","created":{"date-parts":[[2012,11,18]],"date-time":"2012-11-18T02:50:02Z","timestamp":1353207002000},"page":"264-265","source":"Crossref","is-referenced-by-count":15,"title":["VAGUE: a graphical user interface for the Velvet assembler"],"prefix":"10.1093","volume":"29","author":[{"given":"David R.","family":"Powell","sequence":"first","affiliation":[{"name":"1 Victorian Bioinformatics Consortium, Monash University, Clayton 3800, Australia and 2Life Sciences Computation Centre, Victorian Life Sciences Computation Initiative, Parkville 3053, Australia"},{"name":"1 Victorian Bioinformatics Consortium, Monash University, Clayton 3800, Australia and 2Life Sciences Computation Centre, Victorian Life Sciences Computation Initiative, Parkville 3053, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Torsten","family":"Seemann","sequence":"additional","affiliation":[{"name":"1 Victorian Bioinformatics Consortium, Monash University, Clayton 3800, Australia and 2Life Sciences Computation Centre, Victorian Life Sciences Computation Initiative, Parkville 3053, Australia"},{"name":"1 Victorian Bioinformatics Consortium, Monash University, Clayton 3800, Australia and 2Life Sciences Computation Centre, Victorian Life Sciences Computation Initiative, Parkville 3053, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2012,11,17]]},"reference":[{"key":"2023012810173446400_bts664-B1","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1101\/gr.074492.107","article-title":"Velvet: algorithms for de novo short read assembly using de Bruijn graphs","volume":"18","author":"Zerbino","year":"2008","journal-title":"Genome Res."},{"key":"2023012810173446400_bts664-B2","doi-asserted-by":"crossref","first-page":"e8407","DOI":"10.1371\/journal.pone.0008407","article-title":"Pebble and rock band: heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler","volume":"4","author":"Zerbino","year":"2009","journal-title":"PLoS One"},{"key":"2023012810173446400_bts664-B3","doi-asserted-by":"crossref","DOI":"10.1002\/0471250953.bi1105s31","article-title":"Using the Velvet de novo assembler for short-read sequencing technologies","author":"Zerbino","year":"2010","journal-title":"Curr. Protoc. Bioinformatics"},{"key":"2023012810173446400_bts664-B4","doi-asserted-by":"crossref","first-page":"e17915","DOI":"10.1371\/journal.pone.0017915","article-title":"A practical comparison of de novo genome assembly software tools for next-generation sequencing technologies","volume":"6","author":"Zhang","year":"2011","journal-title":"PLoS One"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/2\/264\/48890638\/bioinformatics_29_2_264.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/2\/264\/48890638\/bioinformatics_29_2_264.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,28]],"date-time":"2023-01-28T10:17:56Z","timestamp":1674901076000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/29\/2\/264\/202039"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,11,17]]},"references-count":4,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2013,1,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bts664","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2013,1,15]]},"published":{"date-parts":[[2012,11,17]]}}}