TY - JOUR
T1 - Supercomputing for the parallelization of whole genome analysis
AU - Puckelwartz, Megan J.
AU - Pesce, Lorenzo L.
AU - Nelakuditi, Viswateja
AU - Dellefave-Castillo, Lisa
AU - Golbus, Jessica R.
AU - Day, Sharlene M.
AU - Cappola, Thomas P.
AU - Dorn, Gerald W.
AU - Foster, Ian T.
AU - Mcnally, Elizabeth M.
N1 - Funding Information:
Funding: This work was supported in part by National Institutes of Health through resources provided by the Computation Institute and the Biological Sciences Division of the University of Chicago and Argonne National Laboratory [S10 RR029030-01], and NIH AR052646, NIH HL61322, NIH NS072027, and the Doris Duke Charitable Foundation.
PY - 2014/6/1
Y1 - 2014/6/1
N2 - Motivation: The declining cost of generating DNA sequence is promoting an increase in whole genome sequencing, especially as applied to the human genome. Whole genome analysis requires the alignment and comparison of raw sequence data, and results in a computational bottleneck because of limited ability to analyze multiple genomes simultaneously. Results: We now adapted a Cray XE6 supercomputer to achieve the parallelization required for concurrent multiple genome analysis. This approach not only markedly speeds computational time but also results in increased usable sequence per genome. Relying on publically available software, the Cray XE6 has the capacity to align and call variants on 240 whole genomes in ∼50 h. Multisample variant calling is also accelerated.
AB - Motivation: The declining cost of generating DNA sequence is promoting an increase in whole genome sequencing, especially as applied to the human genome. Whole genome analysis requires the alignment and comparison of raw sequence data, and results in a computational bottleneck because of limited ability to analyze multiple genomes simultaneously. Results: We now adapted a Cray XE6 supercomputer to achieve the parallelization required for concurrent multiple genome analysis. This approach not only markedly speeds computational time but also results in increased usable sequence per genome. Relying on publically available software, the Cray XE6 has the capacity to align and call variants on 240 whole genomes in ∼50 h. Multisample variant calling is also accelerated.
UR - http://www.scopus.com/inward/record.url?scp=84901335692&partnerID=8YFLogxK
U2 - 10.1093/bioinformatics/btu071
DO - 10.1093/bioinformatics/btu071
M3 - Article
C2 - 24526712
AN - SCOPUS:84901335692
SN - 1367-4803
VL - 30
SP - 1508
EP - 1513
JO - Bioinformatics
JF - Bioinformatics
IS - 11
ER -