{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,27]],"date-time":"2026-06-27T15:34:27Z","timestamp":1782574467011,"version":"3.54.5"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"14","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1213,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Because an enormous amount of sequence data is being collected, a method to effectively display sequence variation information is urgently needed. tasuke is a web application that visualizes large-scale resequencing data generated by next-generation sequencing technologies and is suitable for rapid data release to the public on the web. The variation and read depths of multiple genomes, as well as annotations, can be shown simultaneously at various scales. We demonstrate the use of TASUKE by applying it to 50 rice and 100 human genome resequencing datasets.<\/jats:p>\n               <jats:p>Availability and implementation: The tasuke program package and user manual are available from http:\/\/tasuke.dna.affrc.go.jp\/.<\/jats:p>\n               <jats:p>Contact: \u00a0taitoh@affrc.go.jp<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt295","type":"journal-article","created":{"date-parts":[[2013,6,8]],"date-time":"2013-06-08T01:09:41Z","timestamp":1370653781000},"page":"1806-1808","source":"Crossref","is-referenced-by-count":34,"title":["<scp>Tasuke<\/scp>: a web-based visualization program for large-scale resequencing data"],"prefix":"10.1093","volume":"29","author":[{"given":"Masahiko","family":"Kumagai","sequence":"first","affiliation":[{"name":"1 Bioinformatics Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan and 2DYNACOM Co., Ltd. Chiba, Chiba 261-7125, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jungsok","family":"Kim","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan and 2DYNACOM Co., Ltd. Chiba, Chiba 261-7125, Japan"},{"name":"1 Bioinformatics Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan and 2DYNACOM Co., Ltd. Chiba, Chiba 261-7125, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ryutaro","family":"Itoh","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan and 2DYNACOM Co., Ltd. Chiba, Chiba 261-7125, Japan"},{"name":"1 Bioinformatics Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan and 2DYNACOM Co., Ltd. Chiba, Chiba 261-7125, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Takeshi","family":"Itoh","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan and 2DYNACOM Co., Ltd. Chiba, Chiba 261-7125, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2013,6,7]]},"reference":[{"key":"2023012810454241300_btt295-B1","doi-asserted-by":"crossref","first-page":"80","DOI":"10.4161\/fly.19695","article-title":"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3","volume":"6","author":"Cingolani","year":"2012","journal-title":"Fly (Austin)"},{"key":"2023012810454241300_btt295-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":"2023012810454241300_btt295-B3","doi-asserted-by":"crossref","first-page":"1938","DOI":"10.1093\/bioinformatics\/btq332","article-title":"Savant: genome browser for high-throughput sequencing data","volume":"26","author":"Fiume","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012810454241300_btt295-B4","doi-asserted-by":"crossref","first-page":"D48","DOI":"10.1093\/nar\/gks1236","article-title":"Ensembl 2013","volume":"41","author":"Flicek","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2023012810454241300_btt295-B5","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1007\/978-1-4419-5913-3_15","article-title":"Biological databases at DNA data bank of Japan in the era of next-generation sequencing technologies","volume":"680","author":"Kodama","year":"2010","journal-title":"Adv. Exp. Med. Biol."},{"key":"2023012810454241300_btt295-B6","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012810454241300_btt295-B7","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012810454241300_btt295-B8","doi-asserted-by":"crossref","first-page":"2983","DOI":"10.1093\/bioinformatics\/bts557","article-title":"VarB: a variation browsing and analysis tool for variants derived from next-generation sequencing data","volume":"28","author":"Preston","year":"2012","journal-title":"Bioinformatics"},{"key":"2023012810454241300_btt295-B9","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/pcp\/pcs183","article-title":"Rice annotation project database (RAP-DB): an integrative and interactive database for rice genomics","volume":"54","author":"Sakai","year":"2013","journal-title":"Plant Cell Physiol."},{"key":"2023012810454241300_btt295-B10","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1093\/bib\/bbs017","article-title":"Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration","volume":"14","author":"Thorvaldsd\u00f3ttir","year":"2013","journal-title":"Brief. Bioinform."},{"key":"2023012810454241300_btt295-B11","first-page":"1","article-title":"Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes","volume":"30","author":"Xu","year":"2011","journal-title":"Nat. Biotechnol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/14\/1806\/48889580\/bioinformatics_29_14_1806.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/14\/1806\/48889580\/bioinformatics_29_14_1806.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,28]],"date-time":"2023-01-28T12:30:01Z","timestamp":1674909001000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/29\/14\/1806\/233205"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,6,7]]},"references-count":11,"journal-issue":{"issue":"14","published-print":{"date-parts":[[2013,7,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btt295","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2013,7,15]]},"published":{"date-parts":[[2013,6,7]]}}}