Scaling read aligners to hundreds of threads on general-purpose processors

Bioinformatics
Ben LangmeadRone Charles

Abstract

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. 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. Experiments for this study: https://github.com/BenLangmead/bowtie-scaling. http://bowtie-bio.sourceforge.net. http://bowtie-bio.sourceforge.net/bowtie2. http://www.ccb.jhu.edu/software/hisat. Supplementary data are available at Bioinformatics online.

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Citations

Nov 26, 2019·Molecular Plant-microbe Interactions : MPMI·Si-Qi TaoSébastien Duplessis
Oct 9, 2019·The Journal of Biological Chemistry·Lukas J TroxlerMarkus Hilty
Dec 14, 2019·Acta Parasitologica·Huali SongXiaoyan Zhang
Feb 9, 2020·Applied and Environmental Microbiology·Julia M McGonigleWilliam J Brazelton
Feb 26, 2019·Microbiology Resource Announcements·Christina J CastroJan Vinjé
May 14, 2020·Molecular Biology of the Cell·Kaitlin P KoreskiRobert J Duronio
Jun 9, 2020·Environmental Microbiology·Pascal AlonsoChristian Vernière
Sep 10, 2020·Proceedings of the National Academy of Sciences of the United States of America·Rachel M WheatleyPhilip S Poole
Apr 15, 2019·Human Genetics·Irfan UllahSuzanne M Leal
Dec 11, 2019·Nature Microbiology·J Cesar Ignacio-EspinozaJed A Fuhrman
Nov 30, 2019·Genome Biology·Derrick E WoodBen Langmead
Aug 13, 2020·Nature Communications·José M GómezRubén Torices
Nov 2, 2019·Nucleic Acids Research·James J DavisRick Stevens
Mar 12, 2020·Proceedings of the National Academy of Sciences of the United States of America·Philipp RaffeinerPeter K Vogt
Aug 12, 2020·Proceedings of the National Academy of Sciences of the United States of America·Yaqun XinNicolas Gompel
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Apr 12, 2020·Bioinformatics·Marco OlivaMattia Prosperi
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Nov 13, 2020·Biotechnology and Bioengineering·Norichika OgataTakeshi Omasa
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Mar 4, 2020·The Journal of Clinical Investigation·Giorgia AlvisiEnrico Lugli

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Datasets Mentioned

BETA
ERR194147
SRR069520
SRR3947551

Methods Mentioned

BETA
chip

Software Mentioned

Bowtie
FASTQ
MEM
XSEDE
Intel Thread Building Blocks ( TBB ) library
TBB
HISAT
Cilk
Bowtie 2
TinyThread

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