Can pilon work with an assembly with ambiguous bases?

broadinstitute / pilon

Pilon is an automated genome assembly improvement and variant detection tool

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Can pilon work with an assembly with ambiguous bases? #49

Closed caonetto closed 7 years ago

caonetto commented 7 years ago

Hi, I merged multiple nanopore contigs using illumina data but I have some ambiguous bases in the final contig. I want to polish this final contig with the original illumina data. Will pilon work with this ambiguous bases?

Thanks!

w1bw commented 7 years ago

I believe Pilon will "correct" those bases to a non-ambiguous code, assuming it has enough good coverage. If that doesn't seem to be happening, I'll look into it further!