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RemiAllio / MitoFinder

MitoFinder: efficient automated large-scale extraction of mitogenomic data from high throughput sequencing data
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Would it work with Wolbachia (or other symbionts) ? #33

Open sam217pa opened 2 years ago

sam217pa commented 2 years ago

Hi Remi,

I was wondering how mitochondrial-genomes specific is MitoFinder ? Do you think it would work on Wolbachia for instance ? To me it looks like it should, given a set of Wolbachia genes instead of a set of mitochondrial genes. We are looking for integrated and "free-living" Wolbachia, the parallel with NUMTS / free-living mitochondria made me thought we could use mitofinder for this task.

Thanks !

RemiAllio commented 2 years ago

Hi,

Thank you for your message.

Indeed, when I developed MitoFinder I thought about he fact that it could be also used for Wolbachia genomes. That's why I added the option "--new-genes". The specificity of MitoFinder is indeed mainly due to the fact that it is able to read/understand mitochondrial gene names (e.g. COX1=COI) and thus easily create a reference database for further mitochondrial search. The other reason is that mitochondrial genes are (often) monoexonic and thus easier to annotate correctly (I have also added an option for allowing introns but you need a closer reference genome to get accurate results). However, I encourage you to test it by giving a set of annotated Wolbachia genomes as reference and specify the appropriate genetic code and the option "--new-genes" to see if it works. It should at least succeed in catching the contig(s) corresponding to Wolbachia in my opinion. The only constraint is that the annotated gene names of the different reference Wolbachia (if you give more than one) must be identical (MitoFinder is not designed to find synonymy on these genes).

Please let me know if it works and if you are satisfied with the results. I haven't had a chance to try it myself. Best, Rémi

sam217pa commented 2 years ago

Nice ! I'll let you know, probably in 2-3 weeks 🤞

RemiAllio commented 2 years ago

Nice 👍 I look forward to hearing from you! Cheers, Rémi

Andy-B-123 commented 2 years ago

Oooh I would be very interested in your results @sam217pa!

And just a note, thank you @RemiAllio for this program, loving the versatility and annotation output of MitoFinder and working with the data this produces has been a genuine joy!

RemiAllio commented 2 years ago

Thank you @Andy-B-123 for such a positive feedback! Glad you liked it 😃

sam217pa commented 2 years ago

Oops shouldn't have said 3 weeks it's been 21 days already 😬😬😬 we're putting up some controls and a set of "universal" wolbachia core-genome genes to try it out rn, I'll keep you posted @Andy-B-123