Polishing raw nanopore reads with Pacbio

Question

[samuel.a.odonnell]

Hi everyone

I have a rather simple question that I cannot find an answer to, is there a tool available that can polish Nanopore reads with pacbio hifi?

There are already several tools for the same job but using illumina data, but I cannot find one dedicated to pacbio.

Thanks for the help

[GenoMax]

Just a thought. You could make fake illumina reads from HiFi reads.

[samuel.a.odonnell]

As in fragmenting (and pairing) the hifi reads? Do you think this would have any improvement over actual illumina reads?

[GenoMax]

Since only tools available (confirmed by colindaven ) require illumina reads you would be basically creating "illumina like" reads from your HiFi data. This will allow you to try the existing tools. You will want to do this without introducing any additional errors (simulators will allow you to introduce errors). randomreads.sh would be one option from BBMap suite but there are others that could use.

[colindaven]

I don't know of any tools. The more typical polishing approach would be to assemble the ONT reads first, then polish contigs using more accurate shorter reads like Illumina and or with the ONT reads themselves again.

[samuel.a.odonnell]

Thanks for confirming the absence of a tool, I think I can give up the hunt now. I've often done it this typical way of polishing after; however I can generally (and understandably) get better assemblies with polished/corrected reads (and modifying the expected error rate if necessary), so thought polishing with hifi would be ideal.