Confused on PacBio outputs

Question

[Morgan S.]

Hi,

I am trying to figure out which PacBio output to use for SPAdes hybrid assembly. I was given the three .bax.h5 files, the one .bas.h5 file, and the three fastq/fastq files. I have read that currently, the reads are stored in the three .bax.h5 files. So I was going to concat these files and convert the file to fastq. However, now I am second guessing doing that since there is already .fastq files given. Is there a reason why people do not use the already provided .fastq?

Thanks in advance, Morgan

[GenoMax]

Use the fastq files that are provided.

[Morgan S.]

It says that the fastq files are the pre-filtered subreads and that's okay to use?

[GenoMax]

As long as they were pre-filtered to remove the PacBio adapters, which you don't want in your assembly.