{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,9,22]],"date-time":"2023-09-22T18:10:14Z","timestamp":1695406214236},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"9","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Existing SAM visualization tools like \u2018samtools tview\u2019 (Li et al., 2009) are limited to a small region of the genome, and tools like Tablet (Milne et al., 2010) are limited to a relatively small number of reads and may fail outright on large datasets. We need to visualize complex ChIP-Seq and RNA-Seq features such as polarity as well as coverage across whole 3 Gbp genomes such as Human. We have addressed these problems in a lightweight visualization system called SAMSCOPE accelerated by OpenGL. The extensive pre-processing and fast OpenGL interface of SAMSCOPE provides instantaneous and intuitive browsing of complex data at all levels of detail across multiple experiments.<\/jats:p>\n               <jats:p>Availability and implementation: The SAMSCOPE software, implemented in C++ for Linux, with source code, binary packages and documentation are freely available from http:\/\/samscope.dna.bio.keio.ac.jp.<\/jats:p>\n               <jats:p>Contact: \u00a0yasu@bio.keio.ac.jp<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts122","type":"journal-article","created":{"date-parts":[[2012,3,15]],"date-time":"2012-03-15T05:33:56Z","timestamp":1331789636000},"page":"1276-1277","source":"Crossref","is-referenced-by-count":7,"title":["SAMSCOPE: an OpenGL-based real-time interactive scale-free SAM viewer"],"prefix":"10.1093","volume":"28","author":[{"given":"Kris","family":"Popendorf","sequence":"first","affiliation":[{"name":"Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Yokohama, 223-8522, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yasubumi","family":"Sakakibara","sequence":"additional","affiliation":[{"name":"Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Yokohama, 223-8522, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2012,3,13]]},"reference":[{"key":"2023012512225093000_B1","doi-asserted-by":"crossref","first-page":"1011","DOI":"10.1093\/bioinformatics\/btr046","article-title":"SHRiMP2: sensitive yet practical SHort Read Mapping","volume":"27","author":"David","year":"2011","journal-title":"Bioinformatics"},{"key":"2023012512225093000_B2","doi-asserted-by":"crossref","first-page":"2204","DOI":"10.1093\/bioinformatics\/btq351","article-title":"BigWig and BigBed: enabling browsing of large distributed datasets","volume":"26","author":"Kent","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012512225093000_B3","doi-asserted-by":"crossref","first-page":"R25","DOI":"10.1186\/gb-2009-10-3-r25","article-title":"Ultrafast and memory-efficient alignment of short DNA sequences to the human genome","volume":"10","author":"Langmead","year":"2009","journal-title":"Genome Biol."},{"key":"2023012512225093000_B4","doi-asserted-by":"crossref","first-page":"1851","DOI":"10.1101\/gr.078212.108","article-title":"Mapping short DNA sequencing reads and calling variants using mapping quality scores","volume":"18","author":"Li","year":"2008","journal-title":"Genome Res."},{"key":"2023012512225093000_B5","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":"2023012512225093000_B6","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1093\/bioinformatics\/btp666","article-title":"Tablet\u2013next generation sequence assembly visualization","volume":"26","author":"Milne","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012512225093000_B7","doi-asserted-by":"crossref","first-page":"2730","DOI":"10.1093\/bioinformatics\/btp472","article-title":"The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets","volume":"25","author":"Nicol","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012512225093000_B8","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1038\/nmeth.1371","article-title":"Computation for ChIP-seq and RNA-seq studies","volume":"6","author":"Pepke","year":"2009","journal-title":"Nat. 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Graph."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/9\/1276\/48874983\/bioinformatics_28_9_1276.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/9\/1276\/48874983\/bioinformatics_28_9_1276.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T15:52:08Z","timestamp":1674661928000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/28\/9\/1276\/312261"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,3,13]]},"references-count":11,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2012,5,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bts122","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2012,5,1]]},"published":{"date-parts":[[2012,3,13]]}}}