Different contig numbers and contig length generated!

[cheehowteo]

Dear Ruanjue,

Good day!

I am using wtdbg2 for my plant genome assembly. I have run the wtdbg2 with the same PacBio Sequel CLR long reads and same "-x sq" parameters for a few rounds, but the outputs for each rounds are different where I will get different contig number and also different contig size each time. Is this normal for wtdbg2?

My another question is if I want to run the wtdbg2 with my CANU corrected.fasta file, should I use the "-x corrected" parameters mentioned in the wtdbg2 --help?

Thank you.

Best regards, Teo

[ruanjue]

1. The differences are expected in multiple-thread and no harm, because wtdbg2 cannot grant to reproduce the same node set in node-selecting, which is somehow with random. --load-XXX will help you to reduce the duplicated process and reproduce the result.
2. Yes, -x ccs is the best matched preset.