title: Sequence alignment tools: one parallel pattern to rule them all?
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.
authors.affiliation: Computer Science Department, University of Turin, Italy.
authors.forename: Claudia
authors.identifier: 0000-0003-3737-7373
authors.initials: C
authors.lastname: Misale
authors.affiliation: School of Life and Health Sciences, University of Turin, Italy.
authors.forename: Giulio
authors.identifier: 0000-0002-4580-0680
authors.initials: G
authors.lastname: Ferrero
authors.affiliation: Computer Science Department, University of Pisa, Italy.
authors.forename: Massimo
authors.identifier: 0000-0001-6323-3459
authors.initials: M
authors.lastname: Torquati
authors.affiliation: Computer Science Department, University of Turin, Italy.
authors.forename: Marco
authors.identifier: 0000-0001-8788-0829
authors.initials: M
authors.lastname: Aldinucci
mesh_terms: D000465:Algorithms; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software