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Published 20 hours ago • verified publisher icon isovic

Arrow polishing after Racon

Open mictadlo opened this issue 6 years ago • 4 comments

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

Thank you in advance,

Michal

mictadlo avatar Sep 20 '18 23:09 mictadlo

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

rvaser avatar Sep 21 '18 11:09 rvaser

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

peterthorpe5 avatar Nov 10 '18 20:11 peterthorpe5

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

rvaser avatar Nov 11 '18 11:11 rvaser

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

Regards,

Pete

peterthorpe5 avatar Nov 12 '18 09:11 peterthorpe5