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BioMed Research International
Volume 2014, Article ID 539410, 12 pages
http://dx.doi.org/10.1155/2014/539410
Research Article

Sequence Alignment Tools: One Parallel Pattern to Rule Them All?

1Computer Science Department, University of Turin, Italy
2School of Life and Health Sciences, University of Turin, Italy
3Computer Science Department, University of Pisa, Italy

Received 7 March 2014; Revised 3 June 2014; Accepted 21 June 2014; Published 24 July 2014

Academic Editor: Sandra Gesing

Copyright © 2014 Claudia Misale et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

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.