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animal_nr #136
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Thanks for reaching out! We originally designed GetOrganelle, as the name says, for organelle genome assembly. We added Another excuse for not having explored more on nuclear ribosomal RNA is the incomplete concerted evolution issue, which can be painful for many taxa. We even did not include it in our GetOrganelle paper. |
It would be great to add animal_nr to GetOrganelle. I will probably give the anonym approach a try sometime soon, but would be happy to contribute to the overall project. If I develop a database that works, is there a mechanism to compile the results into a shareable database that could be used by others? |
It will be great if you want to contribute to the community with an animal_nr database. GetOrganelleDB is where GetOrganelle pulls the default database and where you may want to fork and share the database. For this, I just added a section https://github.com/Kinggerm/GetOrganelleDB#how-to-contribute to the GetOrganelleDB repository. |
I can confirm that using -F anonym with custom -s and --genes reference files has worked pretty well in my particular case, It would be terrific if this was added as a standard feature. |
Hello, I was wondering about the same issue and, as an animal person, I would love to see updates with animal_nr in the future! |
@gacsinger Hello, I am wondering what fasta file you are using as the seed and what file you are using as the label database? |
Hi people, wanted to ask if there has been any update since the last comment of @gacsinger? Would you still use the anonym function to assemble Ribosomal gene regions in animal WGS data or has there been some sort of standard feature implementation? |
I am wondering if there is a reason the there is no animal_nr seed database. If I want to assembly rRNA gene regions for animals, would I need to build my own? Or is GetOrganelle not an good tool for this?
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