BigWig and BigBed: enabling browsing of large distributed datasets

  • W. J. Kent
    Center for Biomolecular Science and Engineering, School of Engineering, University of California, Santa Cruz (UCSC), Santa Cruz, CA 95064, USA
  • A. S. Zweig
    Center for Biomolecular Science and Engineering, School of Engineering, University of California, Santa Cruz (UCSC), Santa Cruz, CA 95064, USA
  • G. Barber
    Center for Biomolecular Science and Engineering, School of Engineering, University of California, Santa Cruz (UCSC), Santa Cruz, CA 95064, USA
  • A. S. Hinrichs
    Center for Biomolecular Science and Engineering, School of Engineering, University of California, Santa Cruz (UCSC), Santa Cruz, CA 95064, USA
  • D. Karolchik
    Center for Biomolecular Science and Engineering, School of Engineering, University of California, Santa Cruz (UCSC), Santa Cruz, CA 95064, USA

抄録

<jats:title>Abstract</jats:title> <jats:p>Summary: BigWig and BigBed files are compressed binary indexed files containing data at several resolutions that allow the high-performance display of next-generation sequencing experiment results in the UCSC Genome Browser. The visualization is implemented using a multi-layered software approach that takes advantage of specific capabilities of web-based protocols and Linux and UNIX operating systems files, R trees and various indexing and compression tricks. As a result, only the data needed to support the current browser view is transmitted rather than the entire file, enabling fast remote access to large distributed data sets.</jats:p> <jats:p>Availability and implementation: Binaries for the BigWig and BigBed creation and parsing utilities may be downloaded at http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/. Source code for the creation and visualization software is freely available for non-commercial use at http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, implemented in C and supported on Linux. The UCSC Genome Browser is available at http://genome.ucsc.edu</jats:p> <jats:p>Contact:  ann@soe.ucsc.edu</jats:p> <jats:p>Supplementary information: Supplementary byte-level details of the BigWig and BigBed file formats are available at Bioinformatics online. For an in-depth description of UCSC data file formats and custom tracks, see http://genome.ucsc.edu/FAQ/FAQformat.html and http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html</jats:p>

収録刊行物

  • Bioinformatics

    Bioinformatics 26 (17), 2204-2207, 2010-07-17

    Oxford University Press (OUP)

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