Accelerating genome analysis: a primer on an ongoing journey

Simple item page
buir.contributor.authorZülal, Bingöl
buir.contributor.authorAlkan, Can
buir.contributor.authorMutlu, Onur
dc.citation.epage75en_US
dc.citation.issueNumber5en_US
dc.citation.spage65en_US
dc.citation.volumeNumber40en_US
dc.contributor.authorAlser, M.en_US
dc.contributor.authorZülal, Bingölen_US
dc.contributor.authorCali, D. S.en_US
dc.contributor.authorKim, J.en_US
dc.contributor.authorGhose, S.en_US
dc.contributor.authorAlkan, Canen_US
dc.contributor.authorMutlu, Onuren_US
dc.date.accessioned2021-02-11T10:52:19Z
dc.date.available2021-02-11T10:52:19Z
dc.date.issued2020
dc.departmentDepartment of Computer Engineeringen_US
dc.description.abstractGenome analysis fundamentally starts with a process known as read mapping, where sequenced fragments of an organism's genome are compared against a reference genome. Read mapping is currently a major bottleneck in the entire genome analysis pipeline, because state-of-the-art genome sequencing technologies are able to sequence a genome much faster than the computational techniques employed to analyze the genome. We describe the ongoing journey in significantly improving the performance of read mapping. We explain state-of-the-art algorithmic methods and hardware-based acceleration approaches. Algorithmic approaches exploit the structure of the genome as well as the structure of the underlying hardware. Hardware-based acceleration approaches exploit specialized microarchitectures or various execution paradigms (e.g., processing inside or near memory). We conclude with the challenges of adopting these hardware-accelerated read mappers.en_US
dc.identifier.doi10.1109/MM.2020.3013728en_US
dc.identifier.issn0272-1732
dc.identifier.urihttp://hdl.handle.net/11693/55077
dc.language.isoEnglishen_US
dc.publisherIEEEen_US
dc.relation.isversionofhttps://dx.doi.org/10.1109/MM.2020.3013728en_US
dc.source.titleIEEE Microen_US
dc.titleAccelerating genome analysis: a primer on an ongoing journeyen_US
dc.typeArticleen_US
Files
Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
Accelerating_Genome_Analysis_A_Primer_on_an_Ongoing_Journey.pdf
Size:
562.19 KB
Format:
Adobe Portable Document Format
Description:
Download
License bundle
Now showing 1 - 1 of 1
No Thumbnail Available
Name:
license.txt
Size:
1.71 KB
Format:
Item-specific license agreed upon to submission
Description:
Download
Collections
Department of Computer Engineering