MASon (Million Alignments in Seconds) is a C++ library that uses 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.
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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