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NBISweden / Earth-Biogenome-Project-pilot

Assembly and Annotation workflows for analysing data in the Earth Biogenome Project pilot project.
https://www.earthbiogenome.org/
GNU General Public License v3.0
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MitoHiFi module #35

Closed verku closed 10 months ago

verku commented 1 year ago

I've implemented MitoHiFi to assemble mitochondrial genomes from contigs (-c), the alternative option would be to assemble them from the PacBio reads (-r). I decided to do so because then it's possible to use the new MitoHiFi flag -a plant which allows for the assembly of a plant mitogenome. This feature is not optimized yet in the current MitoHiFi version though (see https://github.com/marcelauliano/MitoHiFi#new-parameter-for-plants).

verku commented 10 months ago

At the last nf-core hackathon, we worked on a mitohifi module. It is not finished yet but can be implemented here as soon as it is available.

verku commented 10 months ago

The nf-core MitoHifi module is now available and can be implemented here.

mahesh-panchal commented 10 months ago

Should we close this pull request, or modify this one to add the module? Would you like to add it, or should I?

verku commented 10 months ago

I'd prefer to close this PR and make a new one for the nf-core module. I'm quite busy right now, but if you don't have time to add the module, I can keep it on my to do list and work on that when I have some time in a few weeks from now.

mahesh-panchal commented 10 months ago

OK. Let's close this PR. The issue is still open, so whoever has time first can take it.

verku commented 10 months ago

Sounds good!