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Authors: Tomohiro Yasuda 1 and Asako Koike 2

Affiliations: 1 Hitachi and Litd., Japan ; 2 Hitachi and Ltd., Japan

ISBN: 978-989-758-012-3

Keyword(s): Genome Mapping, Many-core Processor, Multi-threading, Vector Operations.

Related Ontology Subjects/Areas/Topics: Algorithms and Software Tools ; Bioinformatics ; Biomedical Engineering ; Next Generation Sequencing ; Sequence Analysis

Abstract: Next-generation sequencing (NGS) has drastically changed researches based on DNA sequencing with its high throughput and low costs. Mapping sequences generated by NGS sequences onto reference genomes is an indispensable step to find useful knowledge for biological researches or clinical applications. To accelerate genome mapping by using a new many-core processor Xeon Phi, two major mapping programs, BWA and Bowtie2, were ported to Xeon Phi in this study. Although vector operations of Xeon Phi are not compatible with those of x86 processors, these incompatibilities were successfully circumvented. In a computational experiment where the ported programs were evaluated, the performances of the ported BWA and Bowtie2 peaked when 120 and 60 threads were used, respectively. These results imply that performances of BWA and Bowtie2 can be improved by using tens of processing cores.

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Paper citation in several formats:
Yasuda, T. and Koike, A. (2014). Genome Mapping by a 60-core Processor.In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2014) ISBN 978-989-758-012-3, pages 227-232. DOI: 10.5220/0004901702270232

@conference{bioinformatics14,
author={Tomohiro Yasuda. and Asako Koike.},
title={Genome Mapping by a 60-core Processor},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2014)},
year={2014},
pages={227-232},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0004901702270232},
isbn={978-989-758-012-3},
}

TY - CONF

JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2014)
TI - Genome Mapping by a 60-core Processor
SN - 978-989-758-012-3
AU - Yasuda, T.
AU - Koike, A.
PY - 2014
SP - 227
EP - 232
DO - 10.5220/0004901702270232

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