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We've added support for PacBio long-read amplicon sequencing to the devel version of the R package and it seems to work quite well. Preprint: High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution.
I think it will make sense to add this as a tech-specific
To be clear, this is a ways off at this point. Long-read processing won't be possible to add to the plugin until the upcoming R package release propagates to bioconda, and as of now the current R package release isn't even on bioconda yet!