TY - JOUR A2 - Gesing, Sandra AU - Misale, Claudia AU - Ferrero, Giulio AU - Torquati, Massimo AU - Aldinucci, Marco PY - 2014 DA - 2014/07/24 TI - Sequence Alignment Tools: One Parallel Pattern to Rule Them All? SP - 539410 VL - 2014 AB - In this paper, we advocate high-level programming methodology for next generation sequencers (NGS) alignment tools for both productivity and absolute performance. We analyse the problem of parallel alignment and review the parallelisation strategies of the most popular alignment tools, which can all be abstracted to a single parallel paradigm. We compare these tools to their porting onto the FastFlow pattern-based programming framework, which provides programmers with high-level parallel patterns. By using a high-level approach, programmers are liberated from all complex aspects of parallel programming, such as synchronisation protocols, and task scheduling, gaining more possibility for seamless performance tuning. In this work, we show some use cases in which, by using a high-level approach for parallelising NGS tools, it is possible to obtain comparable or even better absolute performance for all used datasets. SN - 2314-6133 UR - https://doi.org/10.1155/2014/539410 DO - 10.1155/2014/539410 JF - BioMed Research International PB - Hindawi Publishing Corporation KW - ER -