importing | analysing pacbio HiFi (CCS) V1-V9 reads

[splaisan (Stephane Plaisance)]

I have Sequel V1-V9 HiFi data (demultiplexed) which I would like to import and process for 16S analysis.
How should I import this fastQ data, I am now using the following command but fear that only the forward reads will be considered when aligning to the database. Also, the sequel gfastq headers are not illumina formated which makes the import complain.

Are there dedicated import type/format which would better fit PB HiFi data?
Is there a tutorial for V1-V9 PB analysis somewhere?

Thanks for feedback

sample-id,absolute-filepath,direction
smpl1,$PWD/reads/demultiplex.bc1005--bc1033.Q20.fastq,forward
smpl2,$PWD/reads/demultiplex.bc1005--bc1035.Q20.fastq,forward


qiime tools import \
  --input-path read_manifest.csv \
  --input-format SingleEndFastqManifestPhred33 \
  --type SampleData[SequencesWithQuality] \
  --output-path read_demux-seq.qza

[andrewsanchez]

Hi @splaisan,

Have you tried searching the forum for previous discussions about PacBio? From what I have gathered, dada2 itself currently supports working with long reads but porting that functionality to q2-dada2 is still underway. Until q2-dada2 is upgraded to wrap the a newer version of dada2, you can work with long-read data in dada2 and then import those results to QIIME 2. That’s what I have seen recommended elsewhere on the forum, at any rate. I hope that helps!

refs:

Add long-read support

add support for Pacbio CCS reads