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

Ben Langmead | Zendy; Christopher Wilks | Zendy; Valentin Antonescu | Zendy; Rone Charles | Zendy

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

Author(s) -

Ben Langmead,

Christopher Wilks,

Valentin Antonescu,

Rone Charles

Publication year - 2018

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/bty648

Subject(s) - computer science , thread (computing) , scaling , software , parallel computing , xeon phi , architecture , operating system , geometry , mathematics , visual arts , art

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.

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