How to use Nanopore and Pacbio simultaneously in CANU?

[gitcruz]

Dear Sergey,

Is nowadays more frequent to have several sources of long-read data. Is there a way to tell canu to use more than 1 type of reads (e.g Pacbio CLR & ONT) at the same time ? could you provide an specific example. would it be possible also to use pacbio-hifi together with nanopore?

If that's the case, how the error rates are set? should be set to the highest one for nanopore: rawErrorRate=0.5 and corrected ErrorRate=0.0145

Thanks,
Fernando

[skoren]

You can mix CLR and ONT, as listed on the quick start: https://canu.readthedocs.io/en/latest/quick-start.html#assembling-with-multiple-technologies-and-multiple-files. Higher error rates win so they'll automatically get set to nanopore tolerance.

If you have recent ONT data on a well-behaved genome or you have a lot more CLR than ONT coverage, you can try to set the error rates lower (e.g. correctedErrorRate=0.105 or correctedErrorRate=0.085) which is primarily a speed optimization.

[gitcruz]

Thanks! F

…

On Mon, 8 Feb 2021 at 16:53, Sergey Koren ***@***.***> wrote: You can mix CLR and ONT, as listed on the quick start: https://canu.readthedocs.io/en/latest/quick-start.html#assembling-with-multiple-technologies-and-multiple-files. Higher error rates win so they'll automatically get set to nanopore tolerance. If you have recent ONT data on a well-behaved genome or you have a lot more CLR than ONT coverage, you can try to set the error rates lower (e.g. correctedErrorRate=0.105 or correctedErrorRate=0.085) which is primarily a speed optimization. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#1892 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB34KVL3FH4SZCBVR5YWYTDS6ACGDANCNFSM4XIW5MRQ> .