SAMSCOPE – a new SAM visualization tool

SAMSCOPE is a lightweight visualization system accelerated by OpenGL designed to visualize complex ChIP-Seq and RNA-Seq features such as polarity as well as coverage across whole 3Gbp genomes such as Human. The extensive preprocessing and fast OpenGL interface of SAMSCOPE provides instantaneous and intuitive browsing of complex data at all levels of detail across multiple experiments. SAMSCOPE overcomes the limitations of existing SAM visualization tools which may be limited to a small region of the genome or a relatively small number of reads.

Availability and Implementation: The SAMSCOPE software, implemented in C++ for Linux, with source code, binary packages, and documentation are freely available from

  • Popendorf K, Sakakibara Y. (2012) SAMSCOPE: An OpenGL based real-time interactive scale-free SAM viewer. Bioinformatics [Epub ahead of print]. [abstract]