Some people have been pushing to use BAM files for unaligned reads too - the upside being that it's a) compressed and b) you know when the file is incomplete as

Some people have been pushing to use BAM files for unaligned reads too - the upside being that it's a) compressed and b) you know when the file is incomplete as the BAM ending is missing. You don't get that with FASTQ. Most notably, the new versions of the PacBio software produce BAM files with the sequencing reads instead of FASTQ (or h5 as previous versions did)