use circlator to fix mitochondrial contig only from canu assembly

[splaisan]

Can I apply circlator to the faulty Mt contig which is present as a partly self overlapping duplicated sequence resulting from assembling the circular chromosome? I have already assembled using canu and would like to correct only that contig Thanks for help

[splaisan]

Should I collect by mapping only the reads contributing to the MT chromosome contig and use them in the circlator pipeline or take all the reads of the project (incl chromosome reads)? I do not want to reassemble the other chromosomes but only correct the self-duplicated MT.

[sjackman]

I have an animal mitochondrial genome assembled by Unicycler (so no overlap). I'd like to orient and rotate the genome to agree with its closest relative in Genbank. I have a FASTA file of the related genome. Is this task possible with Circlator?