parSRA: A framework for the parallel execution of short read aligners on compute clusters
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parSRA: A framework for the parallel execution of short read aligners on compute clustersDate
2018Citation
Jorge González-Domínguez, Christian Hundt, and Bertil Schmidt, "parSRA: A framework for the parallel execution of short read aligners on compute clusters", Journal of Computational Science, vol. 25, pp. 34-139, 2018, doi: https://doi.org/10.1016/j.jocs.2017.01.008
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https://doi.org/10.1016/j.jocs.2017.01.008
Abstract
[Abstract]: The growth of next generation sequencing datasets poses as a challenge to the alignment of reads to reference genomes in terms of both accuracy and speed. In this work we present parSRA, a parallel framework to accelerate the execution of existing short read aligners on distributed-memory systems. parSRA can be used to parallelize a variety of short read alignment tools installed in the system without any modification to their source code. We show that our framework provides good scalability on a compute cluster for accelerating the popular BWA-MEM and Bowtie2 aligners. On average, it is able to accelerate sequence alignments on 16 64-core nodes (in total, 1024 cores) with speedup of 10.48 compared to the original multithreaded tools running with 64 threads on one node. It is also faster and more scalable than the pMap and BigBWA frameworks. Source code of parSRA in C++ and UPC++ running on Linux systems with support for FUSE is freely available at https://sourceforge.net/projects/parsra/.
Keywords
Short read alignment
High performance computing
Multicore clusters
Bioinformatics
PGAS
High performance computing
Multicore clusters
Bioinformatics
PGAS
Description
Esta é a versión aceptada de: Jorge González-Domínguez, Christian Hundt, and Bertil Schmidt, "parSRA: A framework for the parallel execution of short read aligners on compute clusters", Journal of Computational Science, vol. 25, pp. 34-139, 2018, doi: https://doi.org/10.1016/j.jocs.2017.01.008
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Atribución-NoComercial-SinDerivadas 3.0 España © 2017 Elsevier B.V. All rights reserved. This manuscript version is made available under the CC-BY-NC-ND 4.0 license https://creativecommons.org/licenses/bync-
nd/4.0/. This version of the article has been accepted for publication in Journal of Computational Science. The Version of Record is available online at https://
doi.org/10.1016/j.jocs.2017.01.008.