BioHDF pipeline prototype release

Hi everyone,

We are pleased to announce the release of the BioHDF pipeline
prototype, built and tested using HDF5-1.8.4 Patch 1 (with the HDF5
1.6 compatibility flag). This release is intended to demonstrate the
capability of HDF5 to store read, alignment, annotation and reference
sequence data used in analyzing next-generation DNA sequencing (NGS)
data. It is implemented as a set of command-line tools similar to

The BioHDF web page is located here:

This release and some sample data can be obtained from the BioHDF web page at:

Platforms Tested

This release was built and tested on 32- and 64-bit linux systems on
x86/x64 hardware. It has not been tested on Windows though it is
likely to work with Cygwin. It is available as source code only (no

Major Improvements

NCList-based indexing for alignment hits and annotations, ensuring
efficient and correct query results.

SAM/BAM/samtools integration.



Feedback concerning BioHDF can be sent to Dana Robinson at:

    derobins at

We would really like to hear from the NGS and functional genomics
community so please send us your feedback!