{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,15]],"date-time":"2026-04-15T13:54:56Z","timestamp":1776261296526,"version":"3.50.1"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"22","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: The rapid growth of DNA sequencing throughput in recent years implies that graphical interfaces for viewing and correcting errors must now handle large numbers of reads, efficiently pinpoint regions of interest and automate as many tasks as possible. We have adapted consed to reflect this. To allow full-feature editing of large datasets while keeping memory requirements low, we developed a viewer, bamScape, that reads billion-read BAM files, identifies and displays problem areas for user review and launches the consed graphical editor on user-selected regions, allowing, in addition to longstanding consed capabilities such as assembly editing, a variety of new features including direct editing of the reference sequence, variant and error detection, display of annotation tracks and the ability to simultaneously process a group of reads. Many batch processing capabilities have been added.<\/jats:p>\n               <jats:p>Availability: The consed package is free to academic, government and non-profit users, and licensed to others for a fee by the University of Washington. The current version (26.0) is available for linux, macosx and solaris systems or as C++ source code. It includes a user\u2019s manual (with exercises) and example datasets. http:\/\/www.phrap.org\/consed\/consed.html<\/jats:p>\n               <jats:p>Contact: \u00a0dgordon@uw.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt515","type":"journal-article","created":{"date-parts":[[2013,9,1]],"date-time":"2013-09-01T00:34:29Z","timestamp":1377995669000},"page":"2936-2937","source":"Crossref","is-referenced-by-count":294,"title":["<i>Consed:<\/i> a graphical editor for next-generation sequencing"],"prefix":"10.1093","volume":"29","author":[{"given":"David","family":"Gordon","sequence":"first","affiliation":[{"name":"Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA"}]},{"given":"Phil","family":"Green","sequence":"additional","affiliation":[{"name":"Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA"}]}],"member":"286","published-online":{"date-parts":[[2013,8,31]]},"reference":[{"key":"2023012810490168600_btt515-B1","doi-asserted-by":"crossref","first-page":"1699","DOI":"10.1093\/bioinformatics\/btq268","article-title":"Gap5\u2014editing the billion fragment sequence assembly","volume":"26","author":"Bonfield","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012810490168600_btt515-B2","doi-asserted-by":"crossref","first-page":"2156","DOI":"10.1093\/bioinformatics\/btr330","article-title":"The variant call format and VCFtools","volume":"27","author":"Danecek","year":"2011","journal-title":"Bioinformatics"},{"key":"2023012810490168600_btt515-B3","doi-asserted-by":"crossref","first-page":"3907","DOI":"10.1093\/nar\/19.14.3907","article-title":"A sequence assembly and editing program for efficient management of large projects","volume":"19","author":"Dear","year":"1991","journal-title":"Nucleic Acids Res."},{"key":"2023012810490168600_btt515-B4","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1101\/gr.8.3.186","article-title":"Base-calling of automated sequencer traces using phred. 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