{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,28]],"date-time":"2025-10-28T14:49:23Z","timestamp":1761662963425},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"15","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Several new de novo assembly tools have been developed recently to assemble short sequencing reads generated by next-generation sequencing platforms. However, the performance of these tools under various conditions has not been fully investigated, and sufficient information is not currently available for informed decisions to be made regarding the tool that would be most likely to produce the best performance under a specific set of conditions.<\/jats:p>\n               <jats:p>Results: We studied and compared the performance of commonly used de novo assembly tools specifically designed for next-generation sequencing data, including SSAKE, VCAKE, Euler-sr, Edena, Velvet, ABySS and SOAPdenovo. Tools were compared using several performance criteria, including N50 length, sequence coverage and assembly accuracy. Various properties of read data, including single-end\/paired-end, sequence GC content, depth of coverage and base calling error rates, were investigated for their effects on the performance of different assembly tools. We also compared the computation time and memory usage of these seven tools. Based on the results of our comparison, the relative performance of individual tools are summarized and tentative guidelines for optimal selection of different assembly tools, under different conditions, are provided.<\/jats:p>\n               <jats:p>Contact: \u00a0hdeng2@tulane.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr319","type":"journal-article","created":{"date-parts":[[2011,6,3]],"date-time":"2011-06-03T11:53:17Z","timestamp":1307101997000},"page":"2031-2037","source":"Crossref","is-referenced-by-count":95,"title":["Comparative studies of <i>de novo<\/i> assembly tools for next-generation sequencing technologies"],"prefix":"10.1093","volume":"27","author":[{"given":"Yong","family":"Lin","sequence":"first","affiliation":[{"name":"1 Center of System Biomedical Sciences, University of Shanghai for Science and Technology, Shanghai 200093, P. R. China, 2School of Medicine, University of Missouri\u2212Kansas City, Kansas City, MO 64108 and 3Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA"},{"name":"1 Center of System Biomedical Sciences, University of Shanghai for Science and Technology, Shanghai 200093, P. R. China, 2School of Medicine, University of Missouri\u2212Kansas City, Kansas City, MO 64108 and 3Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA"}]},{"given":"Jian","family":"Li","sequence":"additional","affiliation":[{"name":"1 Center of System Biomedical Sciences, University of Shanghai for Science and Technology, Shanghai 200093, P. R. China, 2School of Medicine, University of Missouri\u2212Kansas City, Kansas City, MO 64108 and 3Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA"}]},{"given":"Hui","family":"Shen","sequence":"additional","affiliation":[{"name":"1 Center of System Biomedical Sciences, University of Shanghai for Science and Technology, Shanghai 200093, P. R. China, 2School of Medicine, University of Missouri\u2212Kansas City, Kansas City, MO 64108 and 3Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA"}]},{"given":"Lei","family":"Zhang","sequence":"additional","affiliation":[{"name":"1 Center of System Biomedical Sciences, University of Shanghai for Science and Technology, Shanghai 200093, P. R. China, 2School of Medicine, University of Missouri\u2212Kansas City, Kansas City, MO 64108 and 3Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA"},{"name":"1 Center of System Biomedical Sciences, University of Shanghai for Science and Technology, Shanghai 200093, P. R. China, 2School of Medicine, University of Missouri\u2212Kansas City, Kansas City, MO 64108 and 3Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA"}]},{"given":"Christopher J.","family":"Papasian","sequence":"additional","affiliation":[{"name":"1 Center of System Biomedical Sciences, University of Shanghai for Science and Technology, Shanghai 200093, P. R. China, 2School of Medicine, University of Missouri\u2212Kansas City, Kansas City, MO 64108 and 3Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA"}]},{"given":"Hong\u2212Wen","family":"Deng","sequence":"additional","affiliation":[{"name":"1 Center of System Biomedical Sciences, University of Shanghai for Science and Technology, Shanghai 200093, P. R. China, 2School of Medicine, University of Missouri\u2212Kansas City, Kansas City, MO 64108 and 3Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA"},{"name":"1 Center of System Biomedical Sciences, University of Shanghai for Science and Technology, Shanghai 200093, P. R. China, 2School of Medicine, University of Missouri\u2212Kansas City, Kansas City, MO 64108 and 3Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA"},{"name":"1 Center of System Biomedical Sciences, University of Shanghai for Science and Technology, Shanghai 200093, P. R. China, 2School of Medicine, University of Missouri\u2212Kansas City, Kansas City, MO 64108 and 3Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA"}]}],"member":"286","published-online":{"date-parts":[[2011,6,2]]},"reference":[{"key":"2023012511523889000_B1","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1016\/j.gde.2006.10.009","article-title":"Whole-genome re-sequencing","volume":"16","author":"Bentley","year":"2006","journal-title":"Curr. Opin. Genet. 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