-------------------------------------------------------------------------- The HDF Group Home Page: http://hdfgroup.org/ Helpdesk & Mailing Lists Info: http://hdfgroup.org/services/support.html -------------------------------------------------------------------------- Newsletter #112 April 16, 2010 CONTENTS . Release of BioHDF pipeline prototype - Platforms Tested - Major Improvements - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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: 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. ------------------------------------------------------------- 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!