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• W2952597168 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." @default.
• W2952597168 created "2019-06-27" @default.
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• W2952597168 date "2018-07-18" @default.
• W2952597168 modified "2023-10-16" @default.
• W2952597168 title "Scaling read aligners to hundreds of threads on general-purpose processors" @default.
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• W2952597168 doi "https://doi.org/10.1093/bioinformatics/bty648" @default.
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