The number contig decrease after polishing

[shehongbing]

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]

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