HICOMB 2018, 17th IEEE International Workshop on High Performance Computational Biology, in conjunction with the IEEE International Parallel and Distributed Processing Symposium, 21 May 2018, Vancouver, Canada
Rapid advances in sequencing technologies are producing genomic data on an unprecedented scale. The first, and often one of the most time consuming, step of genomic data analysis is sequence alignment, where sequenced reads must be aligned to a reference genome. Several years of research on alignment algorithms has led to the development of several stateof-the-art sequence aligners that can map tens of thousands of reads per second. In this work, we answer the question "How do sequence aligners utilize modern processors?" We examine four state-ofthe-art aligners running on an Intel processor and identify that all aligners leave the processor substantially underutilized. We perform an in-depth microarchitectural analysis to explore the interaction between aligner software and processor hardware. We identify bottlenecks that lead to processor underutilization
and discuss the implications of our analysis on next-generation sequence aligner design.
Type:
Conférence
City:
Vancouver
Date:
2018-05-21
Department:
Data Science
Eurecom Ref:
5518
Copyright:
© 2018 IEEE. Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from the IEEE.
See also:
