Simulating PacBio long reads and generating consensus

Question

[bdeonovic]

I would like to simulate PacBio long reads and then feed these into PacBio algorithms (I think the appropriate one is quiver, but not sure) to generate a consensus.

I noticed quiver requires data files in h5 format.

What is the best way to proceed? How can I obtain h5 format from my fasta (or fastq) files? Is this even the appropriate workflow?

Answer 1

[bdeonovic]

I found https://github.com/PacificBiosciences/blasr/tree/master/simulator which seems to be a "bas.h5" simulator. This might be what I was looking for.