racon handling of masked bases

isovic / racon

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:

https://github.com/lbcb-sci/racon

MIT License

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racon handling of masked bases #101

Open jonhultqvist opened 5 years ago

jonhultqvist commented 5 years ago

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 commented 5 years ago

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