Orient and rotate mitochondrial genome

tseemann / berokka

🍊 💫 Trim, circularise and orient long read bacterial genome assemblies

GNU General Public License v3.0

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Orient and rotate mitochondrial genome #25

Open sjackman opened 6 years ago

sjackman commented 6 years ago

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 Berokka?

tseemann commented 6 years ago

No, I currently have no orientation support.

I'm not even sure if circlator can do it for an abritrary DNA sequence - i think it needs an ORF and it does tblastn.

sjackman commented 6 years ago

Yeah, I look into circlator too, and came to the same conclusion. I checked and my genome does not start with a coding gene, a tRNA I think (I could confirm).