De novo pacBio genome assembly: How to polish data without quiver?

Question

[Rob]

I am currently working on some de novo genome assembly with pacBio data. I used Canu for assembly but I didn't have access to quiver (or arrow) for data polishing. What can I do now? I can't find any tools for replace quiver, so I'm a little bit stuck...

Thanks !

Answer 1

[colindaven]

A new polisher called ntedit https://github.com/bcgsc/ntEdit is another alternative to RACON and wtdbg2 polishing.

[andorjkiss]

The metrics on this programme look excellent and it's a separate step; after assembly.

Answer 2

[h.mon]

It is an old thread, but as there are no answers on which polishers to use, I will add my experience.

I have tested wtdbg2 polishing module and Racon. Both provided good improvements over either a miniasm or wtdbg2 assemblies - I would imagine they would work fine for a Canu assembly as well. I also performed a Flye assembly, which has a built-in polishing step, and for my data, Flye resulted in the best assembly as per BUSCO evaluation.

Answer 3

[Alex]

Hei,Pacbio have there assembly pipeline ,if you use the canu ,just use the canu to assembly subreads fasta,needn't to polish the reads,canu can do it !

Alex

[Rob]

Well, I use Canu alone, and it don't contain a polisher. I wll try to use the pacBio polisher.

[lakhujanivijay]

Did you find anything for this?