Supercomputing for the parallelization of whole genome analysis

Megan J. Puckelwartz; Lorenzo L. Pesce; Viswateja Nelakuditi; Lisa Dellefave-Castillo; Jessica R. Golbus; Sharlene M. Day; Thomas P. Cappola; Gerald W. Dorn; Ian T. Foster; Elizabeth M. Mcnally

doi:10.1093/bioinformatics/btu071

Supercomputing for the parallelization of whole genome analysis

Megan J. Puckelwartz, Lorenzo L. Pesce, Viswateja Nelakuditi, Lisa Dellefave-Castillo, Jessica R. Golbus, Sharlene M. Day, Thomas P. Cappola, Gerald W. Dorn, Ian T. Foster, Elizabeth M. Mcnally^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

41 Scopus citations

Abstract

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.

Original language	English (US)
Pages (from-to)	1508-1513
Number of pages	6
Journal	Bioinformatics
Volume	30
Issue number	11
DOIs	https://doi.org/10.1093/bioinformatics/btu071
State	Published - Jun 1 2014

Funding

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.

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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title = "Supercomputing for the parallelization of whole genome analysis",

abstract = "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.",

author = "Puckelwartz, {Megan J.} and Pesce, {Lorenzo L.} and Viswateja Nelakuditi and Lisa Dellefave-Castillo and Golbus, {Jessica R.} and Day, {Sharlene M.} and Cappola, {Thomas P.} and Dorn, {Gerald W.} and Foster, {Ian T.} and Mcnally, {Elizabeth M.}",

note = "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.",

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doi = "10.1093/bioinformatics/btu071",

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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.

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Supercomputing for the parallelization of whole genome analysis

Abstract

Funding

ASJC Scopus subject areas

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