Should the assembly be a reference genome?

[elcortegano]

Hi, I'd like to use circlator to assembly a mitochondrion genome. I have (PacBio) reads and "linear" contig-level assemblies for a number of samples, as well as a different "reference" chromosome-level assembly that includes the mitochondrion.

I am not sure how the assembly input files is used in circlator, so not sure either whether that input file should be the "reference" mitochondrion (i.e. the the same for all my samples), or a sample-specific whole-genome assembly . The objective is to detect variation between the mitochondrion assemblies.

Appart from the mitochondrion, would circlator be able to assembly any other extra-chromosomal circular DNA?

Thanks

[phnghia99]

I have the same question, I have multiple "reference" mitogenomes and mitochondrion core genes.
What exactly assembly.fasta input be? And what alternative it should be?