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
samtools.
The BioHDF web page is located here:
http://www.hdfgroup.org/projects/biohdf/
This release and some sample data can be obtained from the BioHDF web page at:
http://www.hdfgroup.org/projects/biohdf/biohdf_downloads.html
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
binaries).
Major Improvements
NCList-based indexing for alignment hits and annotations, ensuring
efficient and correct query results.
SAM/BAM/samtools integration.
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Feedback concerning BioHDF can be sent to Dana Robinson at:
derobins at hdfgroup.org
We would really like to hear from the NGS and functional genomics
community so please send us your feedback!