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The Genomedata format for storing large-scale functional genomics data.

SUMMARY: We present a format for efficient storage of multiple tracks of numeric data anchored to a genome. The format allows fast random access to hundreds of gigabytes of data, while retaining a small disk space footprint. We have also developed utilities to load data into this format. We show that retrieving data from this format is more than 2900 times faster than a naive approach using wiggle files. AVAILABILITY AND IMPLEMENTATION: Reference implementation in Python and C components available at http://noble.gs.washington.edu/proj/genomedata/ under the GNU General Public License.

Pubmed ID: 20435580

Authors

  • Hoffman MM
  • Buske OJ
  • Noble WS

Journal

Bioinformatics (Oxford, England)

Publication Data

June 1, 2010

Associated Grants

  • Agency: NHGRI NIH HHS, Id: HG004695

Mesh Terms

  • Databases, Genetic
  • Genome
  • Genomics
  • Software