SAMSCOPE: an OpenGL-based real-time interactive scale-free SAM viewer.

SUMMARY

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.