Graduate School and Research Center in Digital Sciences

Sequence alignment through the looking glass

Appuswamy, Raja; Fellay, Jacques; Chaturvedi, Nimisha

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.

Document Doi Bibtex

Title:Sequence alignment through the looking glass
Keywords:sequence alignment, computational genomics, microarchitecture
Department:Data Science
Eurecom ref:5518
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Bibtex: @inproceedings{EURECOM+5518, doi = {}, year = {2018}, title = {{S}equence alignment through the looking glass}, author = {{A}ppuswamy, {R}aja and {F}ellay, {J}acques and {C}haturvedi, {N}imisha}, booktitle = {{HICOMB} 2018, 17th {IEEE} {I}nternational {W}orkshop on {H}igh {P}erformance {C}omputational {B}iology, in conjunction with the {IEEE} {I}nternational {P}arallel and {D}istributed {P}rocessing {S}ymposium, 21 {M}ay 2018, {V}ancouver, {C}anada}, address = {{V}ancouver, {CANADA}}, month = {05}, url = {} }
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