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