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
- Hoffman MM
- Buske OJ
- Noble WS
Bioinformatics (Oxford, England)
June 1, 2010
- Agency: NHGRI NIH HHS, Id: HG004695
- Databases, Genetic