GetOrganelle
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Kinggerm
Organelle Genome Assembly Toolkit (Chloroplast/Mitocondrial/ITS)
Hello Dr jin I'm currently trying to assemble a mitogenome from Illumina paired reads. due to the volume of assemblies, I'm running in parallel on a cluster I've had to...
Dear @Kinggerm I use GetOrganelle to assemble the chloroplast of a species and I got 8 fasta files with different length. The fasta and gfa files is below. I hope...
Hello, i'm currently having problems with running GetOrganelle. It works for some species, but not for others. The error i get is: "Error with running SPAdes: == Error == you...
While trying to install GetOrganelle using conda, I am getting following error My network is working fine. I am trying to install it on ubuntu server 20.04 I have updated...
Dear Dr. Jin I am very new to the bioinformatics field, and have recently started using GetOrganelle for my research project. I have been trying to assemble an animal mitochondrial...
Hello, I've encountered an issue which prevents me from reproducing the example code for GetOrganelle. Essentially, it seems that GetOrganelle is searching for the bowtie2 large index file (.bt2l), which...
Seems to me that the databases are currently stored next to the library. This does not work for read-only installations (e.g. containers and multi user installations) and is considered bad...
Dear Sir, I am trying to assemble Mitochondria genome for my plant, and used this tool. I used paired-end dataset, and despite running for sometime, it ended with following message-...
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...
Hi, I have installed using a manual method - git clone etc. But it seems to fail on test data building the bowtie index. Thanks, GetOrganelle v1.7.5.3 get_organelle_from_reads.py assembles organelle...
