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HadrienG / nanoflow

:microscope: De novo assembly of nanopore reads using nextflow
GNU General Public License v3.0
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Racon has changed #12

Closed mictadlo closed 6 years ago

mictadlo commented 6 years ago

Hi, Racon has changed. Do you have any plans to update Racon in your workflow?

Thank you in advance.

Best wishes,

Michal

HadrienG commented 6 years ago

Hi!

Thanks for brining that to my attention. Yes ideally I'd like to switch to versioned docker but haven;t had time to do that yet.

I the meantime I'll update the racon:latest container and process (if needed) asap.

Best, Hadrien

mictadlo commented 6 years ago

Here is an example how to run it (https://github.com/isovic/racon/issues/69#issuecomment-381781156)

HadrienG commented 6 years ago

Hi!

racon should now work again. Note that nanoflow at the moment only performs 1 round of polishing when used with miniasm. If you need several rounds (and are working with bacteria) I recommend running with unicycler, which will perform several racon iterations and only stop when the assembly does not improve anymore.

Best, Hadrien