Question: How to circularize genome assemblies
0
gravatar for Ric
22 months ago by
Ric290
Australia
Ric290 wrote:

Hi, are there any tools which can circularize genome PacBio assemblies/reads? I have an assembly created by miniasm and Racon.

Thank you in advance.

assembly genome • 2.2k views
ADD COMMENTlink modified 7 months ago by predeus1.3k • written 22 months ago by Ric290
3
gravatar for predeus
7 months ago by
predeus1.3k
Russia
predeus1.3k wrote:

If you want to circularize the genome, I'd assume you are assembling a bacterial genome?

If you have pacbio only, best assembler right now is Flye - it's very accurate, does not mess up the circularization, and generates quite nicely finished contigs

If you have pacbio + illumina, Unicycler does a great job especially with plasmids - it rotates and polishes them exhaustively, which works miracles for the accuracy. Could not recommend it enough.

ADD COMMENTlink written 7 months ago by predeus1.3k
1
gravatar for Philipp Bayer
22 months ago by
Philipp Bayer6.6k
Australia/Perth/UWA
Philipp Bayer6.6k wrote:

Yep! It's called circlator

https://github.com/sanger-pathogens/circlator/wiki

ADD COMMENTlink written 22 months ago by Philipp Bayer6.6k
1
gravatar for Kzra
21 months ago by
Kzra30
University of British Columbia
Kzra30 wrote:

Circlator is a great tool. I've also written a program that will circularise a genome simply by looking for most probable repeat sites on either end of the assembly. Unlike Circlator it only requires Python 3 to run, however in cases where the contig hasn't circularised due to a missing region it will not work.

https://github.com/Kzra/Simple-Circularise

ADD COMMENTlink written 21 months ago by Kzra30
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