{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,19]],"date-time":"2026-01-19T08:57:05Z","timestamp":1768813025429,"version":"3.49.0"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"13","license":[{"start":{"date-parts":[[2018,11,22]],"date-time":"2018-11-22T00:00:00Z","timestamp":1542844800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100006769","name":"Russian Science Foundation","doi-asserted-by":"publisher","award":["14-50-00069"],"award-info":[{"award-number":["14-50-00069"]}],"id":[{"id":"10.13039\/501100006769","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Scaffolding is an important step in every genome assembly pipeline, which allows to order contigs into longer sequences using various types of linkage information, such as mate-pair libraries and long reads. In this work, we operate with a notion of a scaffold graph\u2014a graph, vertices of which correspond to the assembled contigs and edges represent connections between them. We present a software package called Scaffold Graph ToolKit that allows to construct and visualize scaffold graphs using different kinds of sequencing data. We show that the scaffold graph appears to be useful for analyzing and assessing genome assemblies, and demonstrate several use cases that can be helpful for both assembly software developers and their users.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>SGTK is implemented in C++, Python and JavaScript and is freely available at https:\/\/github.com\/olga24912\/SGTK.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty956","type":"journal-article","created":{"date-parts":[[2018,11,21]],"date-time":"2018-11-21T13:41:47Z","timestamp":1542807707000},"page":"2303-2305","source":"Crossref","is-referenced-by-count":12,"title":["SGTK: a toolkit for visualization and assessment of scaffold graphs"],"prefix":"10.1093","volume":"35","author":[{"given":"Olga","family":"Kunyavskaya","sequence":"first","affiliation":[{"name":"Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg 199034, Russia"}]},{"given":"Andrey D","family":"Prjibelski","sequence":"additional","affiliation":[{"name":"Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg 199034, Russia"}]}],"member":"286","published-online":{"date-parts":[[2018,11,22]]},"reference":[{"key":"2023051612130236800_bty956-B1","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing","volume":"19","author":"Bankevich","year":"2012","journal-title":"J. Comput. Biol."},{"key":"2023051612130236800_bty956-B2","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1186\/1471-2105-11-345","article-title":"SOPRA: scaffolding algorithm for paired reads via statistical optimization","volume":"11","author":"Dayarian","year":"2010","journal-title":"BMC Bioinform."},{"key":"2023051612130236800_bty956-B3","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-Seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"2023051612130236800_bty956-B5"},{"key":"2023051612130236800_bty956-B4","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1093\/bioinformatics\/btv557","article-title":"Cytoscape.js: a graph theory library for visualisation and analysis","volume":"32","author":"Franz","year":"2016","journal-title":"Bioinformatics"},{"key":"2023051612130236800_bty956-B6","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1186\/s13059-016-0951-y","article-title":"OPERA-LG: efficient and exact scaffolding of large, repeat-rich eukaryotic genomes with performance guarantees","volume":"17","author":"Gao","year":"2016","journal-title":"Genome Biol."},{"key":"2023051612130236800_bty956-B7","doi-asserted-by":"crossref","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","article-title":"QUAST: quality assessment tool for genome assemblies","volume":"29","author":"Gurevich","year":"2013","journal-title":"Bioinformatics"},{"key":"2023051612130236800_bty956-B8","first-page":"7","article-title":"Minimap2: pairwise alignment for nucleotide sequences","volume":"1","author":"Li","year":"2018","journal-title":"Bioinformatics"},{"key":"2023051612130236800_bty956-B9","doi-asserted-by":"crossref","first-page":"3321","DOI":"10.1093\/bioinformatics\/btw379","article-title":"Icarus: visualizer for de novo assembly evaluation","volume":"32","author":"Mikheenko","year":"2016","journal-title":"Bioinformatics"},{"key":"2023051612130236800_bty956-B10","doi-asserted-by":"crossref","first-page":"S5","DOI":"10.1038\/nmeth.1422","article-title":"Visualizing genomes: techniques and challenges","volume":"7","author":"Nielsen","year":"2010","journal-title":"Nat. Methods"},{"key":"2023051612130236800_bty956-B11","doi-asserted-by":"crossref","first-page":"881","DOI":"10.1109\/TVCG.2009.116","article-title":"ABySS-Explorer: visualizing genome sequence assemblies","volume":"15","author":"Nielsen","year":"2009","journal-title":"IEEE Trans. Vis. Computer Graph."},{"key":"2023051612130236800_bty956-B12","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1038\/nbt.1754","article-title":"Integrative genomics viewer","volume":"29","author":"Robinson","year":"2011","journal-title":"Nat. Biotechnol."},{"key":"2023051612130236800_bty956-B13","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1186\/1471-2105-15-281","article-title":"BESST-efficient scaffolding of large fragmented assemblies","volume":"15","author":"Sahlin","year":"2014","journal-title":"BMC Bioinform."},{"key":"2023051612130236800_bty956-B14","doi-asserted-by":"crossref","first-page":"1117","DOI":"10.1101\/gr.089532.108","article-title":"ABySS: a parallel assembler for short read sequence data","volume":"19","author":"Simpson","year":"2009","journal-title":"Genome Res."},{"key":"2023051612130236800_bty956-B15","doi-asserted-by":"crossref","first-page":"3350","DOI":"10.1093\/bioinformatics\/btv383","article-title":"Bandage: interactive visualization of de novo genome assemblies","volume":"31","author":"Wick","year":"2015","journal-title":"Bioinformatics"},{"key":"2023051612130236800_bty956-B16","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":"2023051612130236800_bty956-B17","doi-asserted-by":"crossref","first-page":"2669","DOI":"10.1093\/bioinformatics\/btt476","article-title":"The MaSuRCA genome assembler","volume":"29","author":"Zimin","year":"2013","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/13\/2303\/50340473\/bioinformatics_35_13_2303.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/13\/2303\/50340473\/bioinformatics_35_13_2303.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,16]],"date-time":"2023-05-16T12:13:27Z","timestamp":1684239207000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/35\/13\/2303\/5198892"}},"subtitle":[],"editor":[{"given":"Bonnie","family":"Berger","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2018,11,22]]},"references-count":17,"journal-issue":{"issue":"13","published-print":{"date-parts":[[2019,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty956","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,7,1]]},"published":{"date-parts":[[2018,11,22]]}}}