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Early Perl and BioHDF Work (OBSOLETE)

Perl Wrappers

Sample Perl wrappers to HDF5 were created to illustrate how one might store genomic sequence data in HDF5, and to engage the bioinformatics community in these investigations.

Download the sample Perl wrappers and documentation

The software distribution contains two modules: HDFPerl (wrappers) and BioHDF_Perl (high level APIs).

Performance Study: HDF5 vs. FASTA

A performance study was conducted in which we compare HDF5 with the FASTA format in terms of (a) storage use and (b) time to access genomic sequence data using traditional text-management tools for FASTA and BioHDF_Perl for HDF5. Results show that HDF5 can provide storage efficiency through its use of compression and still allow fast random access through its ability to store indexes along with compressed, chunked data.

Download the performance document (pdf - 160 KB)

- - Last modified: 15 September 2016