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Sequence Alignment Tools : One Parallel Pattern to Rule Them All?
Joint Authors
Misale, Claudia
Torquati, Massimo
Ferrero, Giulio
Aldinucci, Marco
Source
Issue
Vol. 2014, Issue 2014 (31 Dec. 2014), pp.1-12, 12 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2014-07-24
Country of Publication
Egypt
No. of Pages
12
Main Subjects
Abstract EN
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.
American Psychological Association (APA)
Misale, Claudia& Ferrero, Giulio& Torquati, Massimo& Aldinucci, Marco. 2014. Sequence Alignment Tools : One Parallel Pattern to Rule Them All?. BioMed Research International،Vol. 2014, no. 2014, pp.1-12.
https://search.emarefa.net/detail/BIM-479802
Modern Language Association (MLA)
Misale, Claudia…[et al.]. Sequence Alignment Tools : One Parallel Pattern to Rule Them All?. BioMed Research International No. 2014 (2014), pp.1-12.
https://search.emarefa.net/detail/BIM-479802
American Medical Association (AMA)
Misale, Claudia& Ferrero, Giulio& Torquati, Massimo& Aldinucci, Marco. Sequence Alignment Tools : One Parallel Pattern to Rule Them All?. BioMed Research International. 2014. Vol. 2014, no. 2014, pp.1-12.
https://search.emarefa.net/detail/BIM-479802
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-479802