Megan J Puckelwartz1, Lorenzo L Pesce1, Viswateja Nelakuditi1, Lisa Dellefave-Castillo1, Jessica R Golbus1, Sharlene M Day1, Thomas P Cappola1, Gerald W Dorn1, Ian T Foster1, Elizabeth M McNally2. 1. Department of Medicine, Computation Institute and Argonne National Laboratory, 9700 S. Cass Ave. Argonne, IL 60439, USA, Department of Human Genetics, The University of Chicago, 5841 S. Maryland Ave Chicago, IL 60637, USA, Department of Internal Medicine, The University of Michigan, 1150 W Medical Center Dr. Ann Arbor, MI 48109, USA, Perelman School of Medicine, Penn Cardiovascular Institute and Department of Medicine, University of Pennsylvania, 3400 Civic Center Blvd. Philadelphia, PA 19104, USA and Washington University School of Medicine, 660 S. Euclid Ave. St. Louis, MO 63110, USA. 2. Department of Medicine, Computation Institute and Argonne National Laboratory, 9700 S. Cass Ave. Argonne, IL 60439, USA, Department of Human Genetics, The University of Chicago, 5841 S. Maryland Ave Chicago, IL 60637, USA, Department of Internal Medicine, The University of Michigan, 1150 W Medical Center Dr. Ann Arbor, MI 48109, USA, Perelman School of Medicine, Penn Cardiovascular Institute and Department of Medicine, University of Pennsylvania, 3400 Civic Center Blvd. Philadelphia, PA 19104, USA and Washington University School of Medicine, 660 S. Euclid Ave. St. Louis, MO 63110, USADepartment of Medicine, Computation Institute and Argonne National Laboratory, 9700 S. Cass Ave. Argonne, IL 60439, USA, Department of Human Genetics, The University of Chicago, 5841 S. Maryland Ave Chicago, IL 60637, USA, Department of Internal Medicine, The University of Michigan, 1150 W Medical Center Dr. Ann Arbor, MI 48109, USA, Perelman School of Medicine, Penn Cardiovascular Institute and Department of Medicine, University of Pennsylvania, 3400 Civic Center Blvd. Philadelphia, PA 19104, USA and Washington University School of Medicine, 660 S. Euclid Ave. St. Louis, MO 63110, USA.
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. AVAILABILITY AND IMPLEMENTATION: The MegaSeq workflow is designed to harness the size and memory of the Cray XE6, housed at Argonne National Laboratory, for whole genome analysis in a platform designed to better match current and emerging sequencing volume.
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. AVAILABILITY AND IMPLEMENTATION: The MegaSeq workflow is designed to harness the size and memory of the Cray XE6, housed at Argonne National Laboratory, for whole genome analysis in a platform designed to better match current and emerging sequencing volume.
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