Authors:
Tomohiro Yasuda
1
and
Asako Koike
2
Affiliations:
1
Hitachi and Litd., Japan
;
2
Hitachi and Ltd., Japan
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.