Center for Integrative Bioinformatics Vienna
Max F. Perutz Laboratories
Dr. Bohr Gasse 9
A-1030 Vienna, Austria
What is MASon?¶
MASon (Million Alignments in Seconds) is a C++ library that uses the advantages of widely distributed and inexpensive high performance architectures to reduce the computing time of NGS analysis pipelines. MASon employs an optimized SW implementation to align NGS reads and exploits graphic cards (CUDA, OpenCL) and CPU vector instructions (SSE, OpenCL). This allows computation of millions of short local pairwise sequence alignments (36bp - 1,000bp) within a few seconds. MASon can be easily integrated into NGS analysis pipelines and allows programmers to optimally utilize modern hardware, ranging from desktop computers to high-end clusters.
CPU: SSE enabled
How to install prerequisite¶
IMPORTANT: Verify that the PATH environment variable contains the path to the cuda compiler and that LD_LIBRARY_PATH points to the install directory of CUDA.
AMD APP SDK¶
IMPORTANT: Verify that the AMDAPPSDKROOT points to the install path of the AMD APP SDK (default: /opt/AMDAPP).
Source code: mason-rev12.tar.gz
How to build MASon¶
tar xfvz mason-rev12.tar.gz cd mason-trunk/ mkdir -p build/release cd build/release/ cmake -DCMAKE_BUILD_TYPE=Release ../.. make
All binaries are located in mason-trunk/bin.For debug mode use -DCMAKE_BUILD_TYPE=Debug.
MASon was tested on openSUSE 11.4 (x86_64) with GCC 4.3.4 and Ubuntu 11.04/11.10 (x86_64) with GCC 4.4.5.
Rescheneder, P., von Haeseler, A., Sedlazeck, F. J., Mason: Million alignments in seconds, In Proceedings of the International Conference on Bioinformatics: Models, Methods and Algorithms, 2012, Algarve, Portugal, accepted for publication