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.
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.
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.
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.
Yep! It's called circlator
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.