I'm working on a project in which I need to simulate mapping of short reads to long reads of a genome. I have come across this page: https://github.com/PacificBiosciences/GenomicConsensus/blob/master/doc/HowToQuiver.rst which offers a software for the consensus fase of the mapping. However, since I'm trying to do this for the first time, I don't know how to use this. I see that this program wants a cmp.h5 file as input, but how can I generate a file like that? What tools produce files like these? I know these files are a special format originating from PacBio, but how can I produce them?
For example, I have a whole E.Coli genome. I then sequence it using PBSim to produce very short (100 bp) and very long (10k bp) reads in fastq format. Now, I would like to map short ones to each long one and I need consensus software for that. Acutally, I don't even know which software to use for the first fase (before consensus), too (the one which would, I assume, give me as output cmp.h5 file needed by Quiver). Any help appreciated.