In this video from the Intel HPC Developer Conference at SC15, Prof. Dr. Knut Reinert from Freie Universität Berlin presents: The SeqAn C++ library for efficient NGS sequence analysis – applications and HPC modernization using generic programming.
“SeqAn (www.seqan.de) is an open-source C++ template library (BSD license) that implements many efficient and generic data structures and algorithms for Next-Generation Sequencing (NGS) analysis. It contains gapped k-mer indices, enhanced suffix arrays (ESA) or an (bidirectional) FM-index, as well algorithms for fast and accurate alignment or read mapping. Based on those data types and fast I/O routines, users can easily develop tools that are extremely efficient and easy to maintain. Besides multi-core, the research team at Freie Universität Berlin has started generic support for distinguished accelerators such as Intel Xeon Phi in a new IPCC. In this talk we will introduce SeqAn and its generic design, describe successful applications that use SeqAn, and describe how SeqAn will incorporate SIMD and multicore parallelism for its core data structures using the pairwise alignment module as an example.”