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Bioinformatics. 2010 Jun 1;26(11):1458-9. doi: 10.1093/bioinformatics/btq164. Epub 2010 Apr 29.

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

Author information

  • 1Department of Genome Sciences, University of Washington, PO Box 355065, Seattle, WA 98195-5065, USA.

Abstract

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.

PMID:
20435580
[PubMed - indexed for MEDLINE]
PMCID:
PMC2872006
Free PMC Article
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