Dear all,

Could you please advise an end-to-end PacBio pipeline if available?

There are too many pages I visited but I could not find a single end-to-end command line pipeline that takes raw reads as input and performs iso-seq analysis and aligns to a reference genome and get annotations and perform QC and so on.

Including all the necessary example datasets (I mean "all") used in the pipeline with the best practices or suggested thresholds would also help.

If possible something like this workflow with detailed explanations but for PacBio dataset: http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#tximport

thank you !