I have no experience in annotation RNA seq data (or genome assembly) but I've spent the last weeks ploughing through some papers and looking at manuals.
I am wondering why it seems so common that e.g. proprietary pipelines of sequencers are not used?
E.g. the de novo genome assembly pipeline devised by PacBio seems to be cited less than hifiasm or other open source programs. Is this mostly because they are charging a higher price, so people move over to other options, or is it becaue the field is moving at a fast pace and programs are written and benchmarked making the proprietary pipelines obsolete?
1) Is PacBio Iso-Seq annotation a good choice, or is it surpassed by some recently published/improved tool that I haven't read of yet?
2) Using Full-length RNA sequencing to annotate genomes; What are the best performing tools (in terms of speed and accuracy) in 2021 this type of genome annotation?