{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T23:04:34Z","timestamp":1675292674539},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"24","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Recent technological progress has greatly facilitated de novo genome sequencing. However, de novo assemblies consist in many pieces of contiguous sequence (contigs) arranged in thousands of scaffolds instead of small numbers of chromosomes. Confirming and improving the quality of such assemblies is critical for subsequent analysis. We present a method to evaluate genome scaffolding by aligning independently obtained transcriptome sequences to the genome and visually summarizing the alignments using the Cytoscape software. Applying this method to the genome of the red fire ant Solenopsis invicta allowed us to identify inconsistencies in 7%, confirm contig order in 20% and extend 16% of scaffolds.<\/jats:p>\n               <jats:p>Contact: \u00a0oksana.ribagrognuz@unil.ch; yannick.wurm@unil.ch<\/jats:p>\n               <jats:p>Availability: Scripts that generate tables for visualization in Cytoscape from FASTA sequence and scaffolding information files are publicly available at https:\/\/github.com\/ksanao\/TGNet.<\/jats:p>\n               <jats:p>Supplementary Information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr569","type":"journal-article","created":{"date-parts":[[2011,10,13]],"date-time":"2011-10-13T00:14:29Z","timestamp":1318464869000},"page":"3425-3426","source":"Crossref","is-referenced-by-count":8,"title":["Visualization and quality assessment of <i>de novo<\/i> genome assemblies"],"prefix":"10.1093","volume":"27","author":[{"given":"Oksana","family":"Riba-Grognuz","sequence":"first","affiliation":[{"name":"1 Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland, 2Vital-IT Group, Swiss Institute for Bioinformatics, 1015 Lausanne and 3Swiss-Prot Group, Swiss Institute of Bioinformatics, Centre M\u00e9dical Universitaire, 1211 Geneva 4, Switzerland"},{"name":"1 Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland, 2Vital-IT Group, Swiss Institute for Bioinformatics, 1015 Lausanne and 3Swiss-Prot Group, Swiss Institute of Bioinformatics, Centre M\u00e9dical Universitaire, 1211 Geneva 4, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Laurent","family":"Keller","sequence":"additional","affiliation":[{"name":"1 Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland, 2Vital-IT Group, Swiss Institute for Bioinformatics, 1015 Lausanne and 3Swiss-Prot Group, Swiss Institute of Bioinformatics, Centre M\u00e9dical Universitaire, 1211 Geneva 4, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Laurent","family":"Falquet","sequence":"additional","affiliation":[{"name":"1 Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland, 2Vital-IT Group, Swiss Institute for Bioinformatics, 1015 Lausanne and 3Swiss-Prot Group, Swiss Institute of Bioinformatics, Centre M\u00e9dical Universitaire, 1211 Geneva 4, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ioannis","family":"Xenarios","sequence":"additional","affiliation":[{"name":"1 Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland, 2Vital-IT Group, Swiss Institute for Bioinformatics, 1015 Lausanne and 3Swiss-Prot Group, Swiss Institute of Bioinformatics, Centre M\u00e9dical Universitaire, 1211 Geneva 4, Switzerland"},{"name":"1 Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland, 2Vital-IT Group, Swiss Institute for Bioinformatics, 1015 Lausanne and 3Swiss-Prot Group, Swiss Institute of Bioinformatics, Centre M\u00e9dical Universitaire, 1211 Geneva 4, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yannick","family":"Wurm","sequence":"additional","affiliation":[{"name":"1 Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland, 2Vital-IT Group, Swiss Institute for Bioinformatics, 1015 Lausanne and 3Swiss-Prot Group, Swiss Institute of Bioinformatics, Centre M\u00e9dical Universitaire, 1211 Geneva 4, Switzerland"},{"name":"1 Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland, 2Vital-IT Group, Swiss Institute for Bioinformatics, 1015 Lausanne and 3Swiss-Prot Group, Swiss Institute of Bioinformatics, Centre M\u00e9dical Universitaire, 1211 Geneva 4, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2011,10,12]]},"reference":[{"key":"2023012511295933800_B1","doi-asserted-by":"crossref","first-page":"1935","DOI":"10.1093\/molbev\/msq076","article-title":"Gene network visualization and quantitative synteny analysis of more than 300 marine T4-like phage scaffolds from the GOS metagenome","volume":"27","author":"Comeau","year":"2010","journal-title":"Mol. 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