low N50 for pacbio ultra-long reads

[gentlewasp]

Hi Jue,
I used 40X (canu corrected) -67X (uncorrected) pacbio long reads (N50 33-40K) for assembly using wtdbg. Pitfully, I got low N50 of contigs about 80-200K, with different settings (k, p).
It works good on normal pacbio reads (N50 12K).
Should I use special parameters for assembly of untra-long reads?
Thanks
shujun

[ruanjue]

I am not sure. I need to know more about what the difference between ultra-long and normal pacbio reads besiding read length.

[gentlewasp]

Can I send you the untra-long reads for test?

[ruanjue]

No, thanks. It would be nice for you to know more about the data. I am a bit busy now and in fellowing months.

[gentlewasp]

thanks