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ythuang0522 / homopolish

High-quality Nanopore-only genome polisher
GNU General Public License v3.0
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homopolish then modpolish or just modpolish? #54

Closed aldertzomer closed 2 years ago

aldertzomer commented 2 years ago

Should modpolish be run instead of homopolish, or after homopolish?

ythuang0522 commented 2 years ago

Hi @aldertzomer, you should run homopolish first and then modpolish (if you suspect novel modifications). For most cases, homopolish should be sufficient for your needs as it fixes the dominating ONT homopolymer errors (i.e., indels). Modpolish was further developed to correct mismatch/basecalling errors due to novel/unknown modifications, which we spotted in some strains of our bacteria. I hope this helps.

aldertzomer commented 2 years ago

This helps a lot, thank you :)