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lbcb-sci / racon

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads
MIT License
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What will happen if draft contains stretches of Ns? #39

Closed ms-gx closed 4 years ago

ms-gx commented 4 years ago

What will happen if I polish a draft genome which contains stretches of Ns? As for example generated by Flye when scaffolding contigs. It is adding 100 Ns in between if I remember correctly.

I would add parameter "-u" but I assume this has influence on my question.

rvaser commented 4 years ago

Hello, if the stretch of Ns is either at the beginning or end of a 500bp window, it might get truncated. My best bet would be to polish your assembly before scaffolding.

Option -u is used when you want all of your contigs in the output file, otherwise those that are not polished at all will be dropped.

Best regards, Robert

ms-gx commented 4 years ago

Thank you for the quick response! Yes, in the meantime I saw that racon truncates those stretches of Ns. There is no way to avoid this I guess?

rvaser commented 4 years ago

Actually, there is the --no-trimming option which does that. Forgot about it :D

ms-gx commented 4 years ago

OK, that sounds promising! So with "--no-trimming" racon will basically just correct regions where it is able to map reads and the others it will leave untouched? I did not really understand this parameter from the help...

rvaser commented 4 years ago

Yes, everything that can be corrected with the reads will be, and nothing shall be trimmed away due to low coverage.

ms-gx commented 4 years ago

OK, many thanks!