Document Detail


SAMSCOPE: an OpenGL-based real-time interactive scale-free SAM viewer.
MedLine Citation:
PMID:  22419785     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Existing SAM visualization tools like 'samtools tview' (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. 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.
Authors:
Kris Popendorf; Yasubumi Sakakibara
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Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't     Date:  2012-03-13
Journal Detail:
Title:  Bioinformatics (Oxford, England)     Volume:  28     ISSN:  1367-4811     ISO Abbreviation:  Bioinformatics     Publication Date:  2012 May 
Date Detail:
Created Date:  2012-04-30     Completed Date:  2012-12-07     Revised Date:  2013-05-20    
Medline Journal Info:
Nlm Unique ID:  9808944     Medline TA:  Bioinformatics     Country:  England    
Other Details:
Languages:  eng     Pagination:  1276-7     Citation Subset:  IM    
Affiliation:
Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Yokohama, Japan.
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MeSH Terms
Descriptor/Qualifier:
Animals
Bacillus subtilis / genetics
Computer Graphics*
Genome
Humans
Programming Languages
Sequence Alignment / methods*
Sequence Analysis, DNA / methods*
Software*

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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