How to check the version of PacBio HiFi genomic reads?

Question

[draccident]

I am trying to check which version of PacBio HiFi genomic reads I have as Minimap2 has different input functions depending on the version number. Does anyone know how this information would be obtained? It's likely I have 2.19 since they were produced last year, but it would be ideal to check.

./minimap2 -ax map-hifi ref.fa pacbio-ccs.fq.gz > aln.sam # PacBio HiFi/CCS genomic reads (v2.19 or later)
./minimap2 -ax asm20 ref.fa pacbio-ccs.fq.gz > aln.sam    # PacBio HiFi/CCS genomic reads (v2.18 or earlier)

Answer 1

[William Rowell]

The version numbers here refer to the version of minimap2, not to the HiFi/CCS version. If you're using minimap2 v2.19 or later, the readme suggests using the -ax map-hifi params.

PacBio recommends using their pbmm2 aligner, which is a front-end for minimap2 with some added features, like allowing native PacBio uBAM input, applying concordance/identity/gap-compressed identity filters, repeated matches trimming, and built-in sorting. For HiFi reads, the pbmm2 align --preset HIFI is recommended for all of our recommended downstream analysis tools.