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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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The number contig decrease after polishing #219

Open shehongbing opened 2 years ago

shehongbing commented 2 years ago

Hi,

I have 300 raw contigs need to be polished. However, only 295 contigs were obtained after polishing with ONT long reads.

besides, the contigs were polished using raw ONT long reads. I was wondering what is the best choose fro ONT long reads, raw reads or corrected long reads uding canu.

Thanks for your kindly help.

Sincerely, Hongbing

rvaser commented 1 year ago

Hello Hongbing, if you want all of your contigs in the output file, regardless of them being polished or not, use option -u/--include-unpolished. You can just use raw reads directly for polishing.

Best regards, Robert