title: SAMSCOPE: an OpenGL-based real-time interactive scale-free SAM viewer.
abstract: CONCLUSIONS
  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.
  
  
  METHODS
  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.affiliation: Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Yokohama, Japan.
authors.forename: Kris
authors.initials: K
authors.lastname: Popendorf
authors.forename: Yasubumi
authors.initials: Y
authors.lastname: Sakakibara
mesh_terms: D000818:Animals; D001412:Bacillus subtilis / Q000235:genetics; D003196:Computer Graphics; D016678:Genome; D006801:Humans; D011381:Programming Languages; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software