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isovic / racon

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:
https://github.com/lbcb-sci/racon
MIT License
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Arrow polishing after Racon #91

Open mictadlo opened 6 years ago

mictadlo commented 6 years ago

Hi all, Does it make sense to run arrow polishing after a hybrid assembly (w2rap-contiger/DGB2OLC) and Racon?

Thank you in advance,

Michal

rvaser commented 6 years ago

Hi Michal, it depends on the order of polishing. If you run PB Racon - PB Arrow - Illumina Racon, I think you should be fine (if you have decent PB coverage).

Best regards, Robert

peterthorpe5 commented 5 years ago

Dear Robert,

Can you use Racon as an alternative to Arrow? The run time of Arrow and the pacbio style bam they require is very time consuming. I will be polishing with Illumina and Pilon after. Please let me know your thoughts,

Regards,

Peter Thorpe

rvaser commented 5 years ago

Hi Peter, Racon only uses base qualities (if they are present) so you won't get the same accuracy level as with Arrow. But if you have Illumina data, I think you can skip Arrow polishing. You can use Racon for Illumina polishing as well.

Best regards, Robert

peterthorpe5 commented 5 years ago

Thank you very much for your reply Robert. It is good that Racon can do Illumina polishing.

Regards,

Pete