University of Illinois Urbana-Champaign

Decomposing Genomics Algorithms: Core Computations for Accelerating Genomics

Athreya, Arjun P.; Banerjee, Subho S.; Jongeneel, C. Victor; Kalbarczyk, Zbigniew T.; Iyer, Ravishankar K.

Content Files
UILU-ENG-14-2201.pdf

Permalink

https://hdl.handle.net/2142/90442

Description

Title
Decomposing Genomics Algorithms: Core Computations for Accelerating Genomics
Author(s)
  • Athreya, Arjun P.
  • Banerjee, Subho S.
  • Jongeneel, C. Victor
  • Kalbarczyk, Zbigniew T.
  • Iyer, Ravishankar K.
Issue Date
2014-02
Keyword(s)
  • Bioinformatics
  • Genomic analyses
  • Algorithms
Date of Ingest
  • 2016-07-07T14:59:31Z
  • 2017-07-14T23:13:37Z
Abstract
Technological advances in genomic analyses and computing sciences has led to a burst in genomics data. With those advances, there has also been parallel growth in dedicated accelerators for specific genomic analyses. However, biologists are in need of a reconfigurable machine that can allow them to perform multiple analyses without needing to go for dedicated compute platforms for each analysis. This work addresses the first steps in the design of such a reconfigurable machine. We hypothesize that this machine design can consist of some accelerators of computations common across various genomic analyses. This work studies a subset of genomic analyses and identifies such core computations. We further investigate the possibility of further accelerating through a deeper analysis of the computation primitives.
Publisher
Coordinated Science Laboratory, University of Illinois at Urbana-Champaign
Series/Report Name or Number
Coordinated Science Laboratory Report no. UILU-ENG-14-2201
Type of Resource
text
Genre of Resource
Technical Report
Language
en
Permalink
http://hdl.handle.net/2142/90442
Sponsor(s)/Grant Number(s)
National Science Foundation (NSF CNS 13-37732); Infosys; IBM Faculty Award; Office of the Vice Chancellor for Research, University of Illinois at Urbana-Champaign

Owning Collections

Report - Coordinated Science Laboratory PRIMARY