read of insert VS circular consensus sequence

Question

[arnauperis92]

Hi all,

I am starting with PacBio pipelines and I got stuck when trying to understand which is the difference between Read Of Insert (ROI) and Circular Consensus Sequence (CCS). I took a look at the documentation and several papers, but the way they define those terms is very confusing and not clear to me. Does anyone has an idea of which is the exact difference between both terms?

Thank you very much in advance! AP

[gconcepcion]

Read of Insert (ROI) & Circular Consensus Sequences (CCS) for all intents and purposes can be thought of as conceptually as similar things. A CCS read is really just a special case of a Read of Insert where the number of full passes over the subread is 2 or greater. In contrast a read of insert is just the highest quality sequence for a particular insert. In the case of multiple full passes, a consensus sequence is generated from the overlapping subreads representing the ROI. However some ZMWs only have one single full pass and a partial pass so no consensus can be called. When this is the case, the full subread constitutes the ROI and there is no actual consensus being called among the subreads. Read of Insert is an antiquated term that the company was using for a couple of years before it fell out of use in favor of CCS reads & HiFi reads (which are a further subset of high quality CCS reads of >99.9% accuracy or greater). You should see decreasing usage of the term ROI as the technology further matures and the backlog of older peer reviewed literature starts to fade in favor of newer HiFi data.

[arnauperis92]

Got it! Thank you very much for your explanation, it really helps!