Good day. I am terribly new to bioinformatics and sequencing. Last week I received the reads for my gut microbiome samples. These were sequenced using the PacBio sequel II - generating CCS. The provider has given me the fastq files. I'm just a bit lost from here. Which is the best workflow/platform to demultiplex. I'm most comfortable in R, but as far as I'm aware I first need to clean up the sequences before I can import to R.

I've been searching, and Usearch seems to be quite popular/user-friendly.

Any advice is appreciated. Thanks

edit: spelling/tags