Please see The HDF Group's new Support Portal for the latest information.
CONTENTS
Release of BioHDF pipeline prototype
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:
https://support.hdfgroup.org/projects/biohdf/
This release and some sample data can be obtained from the BioHDF web page at:
https://support.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.
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!
- - Last modified: 14 October 2016