{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,2]],"date-time":"2026-06-02T08:01:51Z","timestamp":1780387311715,"version":"3.54.1"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"19","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1888,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.5"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: High-throughput DNA sequencing technologies have spurred the development of numerous novel methods for genome assembly. With few exceptions, these algorithms are heuristic and require one or more parameters to be manually set by the user. One approach to parameter tuning involves assembling data from an organism with an available high-quality reference genome, and measuring assembly accuracy using some metrics.<\/jats:p>\n               <jats:p>We developed a system to measure assembly quality under several scoring metrics, and to compare assembly quality across a variety of assemblers, sequence data types, and parameter choices. When used in conjunction with training data such as a high-quality reference genome and sequence reads from the same organism, our program can be used to manually identify an optimal sequencing and assembly strategy for de novo sequencing of related organisms.<\/jats:p>\n               <jats:p>Availability: GPL source code and a usage tutorial is at http:\/\/ngopt.googlecode.com<\/jats:p>\n               <jats:p>Contact: \u00a0aarondarling@ucdavis.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data is available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr451","type":"journal-article","created":{"date-parts":[[2011,8,3]],"date-time":"2011-08-03T02:01:04Z","timestamp":1312336864000},"page":"2756-2757","source":"Crossref","is-referenced-by-count":106,"title":["Mauve Assembly Metrics"],"prefix":"10.1093","volume":"27","author":[{"given":"Aaron E.","family":"Darling","sequence":"first","affiliation":[{"name":"1 Genome Center, 2Department of Evolution and Ecology, 3Medical Microbiology and Immunology, 4Biomedical Engineering, University of California-Davis, Davis, CA 95616, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew","family":"Tritt","sequence":"additional","affiliation":[{"name":"1 Genome Center, 2Department of Evolution and Ecology, 3Medical Microbiology and Immunology, 4Biomedical Engineering, University of California-Davis, Davis, CA 95616, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonathan A.","family":"Eisen","sequence":"additional","affiliation":[{"name":"1 Genome Center, 2Department of Evolution and Ecology, 3Medical Microbiology and Immunology, 4Biomedical Engineering, University of California-Davis, Davis, CA 95616, USA"},{"name":"1 Genome Center, 2Department of Evolution and Ecology, 3Medical Microbiology and Immunology, 4Biomedical Engineering, University of California-Davis, Davis, CA 95616, USA"},{"name":"1 Genome Center, 2Department of Evolution and Ecology, 3Medical Microbiology and Immunology, 4Biomedical Engineering, University of California-Davis, Davis, CA 95616, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marc T.","family":"Facciotti","sequence":"additional","affiliation":[{"name":"1 Genome Center, 2Department of Evolution and Ecology, 3Medical Microbiology and Immunology, 4Biomedical Engineering, University of California-Davis, Davis, CA 95616, USA"},{"name":"1 Genome Center, 2Department of Evolution and Ecology, 3Medical Microbiology and Immunology, 4Biomedical Engineering, University of California-Davis, Davis, CA 95616, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2011,8,2]]},"reference":[{"key":"2023012512011097700_B1","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search 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