Scaling read aligners to hundreds of threads on general-purpose processors
B Langmead, C Wilks, V Antonescu, R Charles - Bioinformatics, 2019 - academic.oup.com
B Langmead, C Wilks, V Antonescu, R Charles
Bioinformatics, 2019•academic.oup.comMotivation General-purpose processors can now contain many dozens of processor cores
and support hundreds of simultaneous threads of execution. To make best use of these
threads, genomics software must contend with new and subtle computer architecture issues.
We discuss some of these and propose methods for improving thread scaling in tools that
analyze each read independently, such as read aligners. Results We implement these
methods in new versions of Bowtie, Bowtie 2 and HISAT. We greatly improve thread scaling …
and support hundreds of simultaneous threads of execution. To make best use of these
threads, genomics software must contend with new and subtle computer architecture issues.
We discuss some of these and propose methods for improving thread scaling in tools that
analyze each read independently, such as read aligners. Results We implement these
methods in new versions of Bowtie, Bowtie 2 and HISAT. We greatly improve thread scaling …
Motivation
General-purpose processors can now contain many dozens of processor cores and support hundreds of simultaneous threads of execution. To make best use of these threads, genomics software must contend with new and subtle computer architecture issues. We discuss some of these and propose methods for improving thread scaling in tools that analyze each read independently, such as read aligners.
Results
We implement these methods in new versions of Bowtie, Bowtie 2 and HISAT. We greatly improve thread scaling in many scenarios, including on the recent Intel Xeon Phi architecture. We also highlight how bottlenecks are exacerbated by variable-record-length file formats like FASTQ and suggest changes that enable superior scaling.
Availability and implementation
Experiments for this study: https://github.com/BenLangmead/bowtie-scaling.
Bowtie
http://bowtie-bio.sourceforge.net .
Bowtie 2
http://bowtie-bio.sourceforge.net/bowtie2 .
HISAT
http://www.ccb.jhu.edu/software/hisat
Supplementary information
Supplementary data are available at Bioinformatics online.
Oxford University Press