How to circularize genome assemblies

Question

[Ric]

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.

Answer 1

[predeus]

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.

Answer 2

[Kzra]

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

Answer 3

[Philipp Bayer]

Yep! It's called circlator

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