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

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...

Full description

Saved in:
Bibliographic Details
Published in:BioMed research international 2014-01, Vol.2014 (2014), p.1-12
Main Authors: Misale, Claudia, Ferrero, Giulio, Torquati, Massimo, Aldinucci, Marco
Format: Article
Language:English
Subjects:
Algorithms
Biomedical research
DNA sequencing
High-Throughput Nucleotide Sequencing - methods
Humans
Methods
Nucleotide sequencing
Parallel programming (Computer science)
Sequence Alignment - methods
Sequence Analysis, DNA - methods
Software
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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.
ISSN:2314-6133
2314-6141
DOI:10.1155/2014/539410