FWIW, the XSQ format files created by the 5500 Series ABI SOLiD are HDF5, but not BioHDF:Probably not, as it is somewhat a competitor of SAM/BAM (a bit broader in scope, beyond just alignments). As Peter indicated, I know the BioHDF folks (they are here in town); however, my actual question was whether anyone is actually using HDF5 or SRA in production? I haven't seen adoption beyond PacBio, but I have seen some things popping up in Galaxy.
-- ______________ Paul Gordon Bioinformatics Support Specialist Alberta Children's Hospital Research Institute http://www.ucalgary.ca/~gordonp