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Question: De novo pacBio genome assembly: How to polish data without quiver?
1
gravatar for Rob
3.8 years ago by
Rob • 120
Rob • 120 wrote:

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 !
assembly pacbio polishing sequencing quiver • 3.2k views
ADD COMMENT • link •
modified 19 months ago by colindaven • 2.5k • written 3.8 years ago by Rob • 120
3
gravatar for colindaven
19 months ago by
colindaven • 2.5k
Hannover Medical School
colindaven • 2.5k wrote:

A new polisher called ntedit https://github.com/bcgsc/ntEdit is another alternative to RACON and wtdbg2 polishing.
ADD COMMENT • link modified 19 months ago • written 19 months ago by colindaven • 2.5k

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

ADD REPLY • link written 13 months ago by andorjkiss • 20
2
gravatar for h.mon
19 months ago by
h.mon ♦ 32k
Brazil
h.mon ♦ 32k wrote:

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.
ADD COMMENT • link written 19 months ago by h.mon ♦ 32k
0
gravatar for Alex
3.8 years ago by
Alex • 30
America
Alex • 30 wrote:

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
ADD COMMENT • link written 3.8 years ago by Alex • 30

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

ADD REPLY • link written 3.8 years ago by Rob • 120

Did you find anything for this?

ADD REPLY • link written 2.5 years ago by lakhujanivijay ♦ 5.3k
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