racon handling of masked bases

[jonhultqvist]

Hello,

Thank you for developing this great software.

I have a question that I haven't been able to find information about. Is Racon able to handle soft or hardmasked bases? I'm having some issues were paired SNPs and indels are impossible to error-correct using illumina data. I think this could be resolved by finding and masking the SNPs, leaving the indels to be corrected. Is this feasible using Racon?

Best regards Jon

[rvaser]

Hello Jon, I am afraid I did not understand your inquiry. Could you please elaborate? An example would be great.

Sorry for the late response and best regards, Robert