Is it necessary to further run consensus tools on the results of wtdbg or smartdenovo?

[ruanjue]

Is it necessary to further run consensus tools on the results of wtdbg or smartdenovo?

[ruanjue]

Thanks for interesting.

The inside consensus tool wtdbg-cns aims to provide a quick way to reduce sequencing errors. It is suggested to use Quiver and/or Pilon to polish the consensus sequences after you feel happy with the assembly. Usually, wtdbg-cns can reduce error rate down to less than 1%, which can be well-aligned by short reads.

BTW, the paper used strage parameters for wtdbg, limited to say wtdbg always ranked last, I had emailed the author just after its publish.

[YiweiNiu]

Thank you for your reply!

Good to know the error rate of the wtdbg-cns results.

BTW, I know wtdbg and smartdenovo through this paper. After trying several pipelines (Canu, MECAT, miniasm, MaSuRCA, Flye etc.), wtdbg is the fastest and the best (at least the most satisfying N50) so far. I will use the results of wtdbg for downstream analysis.

Thank you for your great tools again!

[ruanjue]

Have a good luck!