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morispi / CONSENT

Scalable long read self-correction and assembly polishing with multiple sequence alignment
https://doi.org/10.1038/s41598-020-80757-5
GNU Affero General Public License v3.0
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Phase retained? #3

Open colindaven opened 5 years ago

colindaven commented 5 years ago

Hi again,

will the phase of the reads be retained following correction ?

i.e. if I want to use the corrected reads for determining phasing and haplotypes , will this information be mixed from the alternative alleles or retained ?

I have used canu before to get nicely corrected reads, sadly the phase information is not retained.

cheers, Colin

morispi commented 5 years ago

Hey,

I haven't tried CONSENT for such a purpose yet, so I can't promise anything.

However, CONSENT was not designed with that purpose in mind. So I believe it will behave like most error correction methods, and mix up the information from the alternative alleles.

Let me know how it goes if you decide to run such an experiment!

Cheers, Pierre