Hi everyone. First, thanks to the developers who made this helpful pipeline possible. I'm planning to use ampliseq to analyse PacBio data. I've been doing this using the functions available in dada2, but I would like to move to your pipeline because this is a more high-throughput and tidy way of running these analyses. For primer removal, I use the function removePrimers, set the reverse complement of the reverse primer (i.e. primer.rev = dada2:::rc(R1492)), and use the option orient = TRUE. In the help from dada2, the developers recommend setting orient = TRUE for PacBio CCS reads because they come in a random mix of forward and reverse-complement orientations. Ampliseq uses cut-adapt for trimming. Does this tool consider the change in the orientation in PacBio reads? Thanks.

Hi there, > Does this tool consider the change in the orientation in PacBio reads? Yes it does. It uses

"--rc -g ${meta.fw_primer}...${meta.rv_primer_revcomp}"

for cutadat here when choosing --pacbio.

Thank you! 👍