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nanoporetech / ont-assembly-polish

ONT assembly and Illumina polishing pipeline
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big genome ? #23

Closed colindaven closed 4 years ago

colindaven commented 4 years ago

Hi,

I have a couple of rat assemblies already I'd like to polish - but not assemble. I assume canu is being used for an initial assembly. Can the canu stage be skipped if an assembly exists already ?

Thanks

bsipos commented 4 years ago

Hi!

I recommend not using this pipeline for your data. I think it would be the best if you did two-three rounds of racon polishing, then medaka, and finally polishing using pilon if you also have Illumina reads.

Best, Botond

colindaven commented 4 years ago

Thanks, we'll write some SLURM scripts ourselves then,