title: Supercomputing for the parallelization of whole genome analysis.
abstract: BACKGROUND
  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.
  
  
  METHODS
  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.
authors: 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.
authors: Megan J
authors: MJ
authors: Puckelwartz
authors: 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.
authors: Lorenzo L
authors: LL
authors: Pesce
authors: 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.
authors: Viswateja
authors: V
authors: Nelakuditi
authors: 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.
authors: Lisa
authors: L
authors: Dellefave-Castillo
authors: 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.
authors: Jessica R
authors: JR
authors: Golbus
authors: 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.
authors: Sharlene M
authors: SM
authors: Day
authors: 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.
authors: Thomas P
authors: TP
authors: Cappola
authors: 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.
authors: Gerald W
authors: GW
authors: Dorn
authors: 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.
authors: Ian T
authors: IT
authors: Foster
authors: 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.
authors: Elizabeth M
authors: EM
authors: McNally
mesh_terms: D003201:Computers; D015894:Genome, Human; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software