output ultra long corrected reads

[chklopp]

Hi,

Is there a parameter to output fully corrected or almost fully corrected UL reads in fasta or fastq format?

Cheers,

[chhylp123]

Hifiasm does not do the base-level correcton for the UL reads, so it cannot output the corrected UL reads.

[chklopp]

Thank you. Do you know at tool which would take hifi + UL and output corrected UL?

What is the impact of the --ul-rate parameter, if I leave default (0.2) for r10.4 reads will it be less efficient to use UL?

[chhylp123]

--ul-rate 0.2 indicates the UL alignment allows at most 20% errors. If r10.4 reads have less number of errors, probably you could have a try with --ul-rate 0.05. This might be able to resolve more repeats or make the UL alignment steps faster.

As for the hybrid correction, I'm not sure if @GuillaumeHolley 's tool could work (see: https://github.com/DecodeGenetics/Ratatosk).

[chklopp]

Thank you.