The workflow performs the alignment of an SMRT cell’s worth of data to a reference. For genomic sequencing data, the workflow also optionally performs CCS correction if the data is from a CCS library but did not get corrected on-instrument. For MAS-seq transcriptome data, this workflow will determine the most likely MAS-seq model, then it will use that model to annotate, segment, and filter the CCS reads. These CCS reads will then be aligned to the reference in trascriptome alignemnt mode. Note:
This is a companion discussion topic for the original entry at github.com/kimkh415/long-read-pipelines/PBFlowcell