Jun 18, 2025

Public workspaceMitogenome Assembly with GetOrganelle

DOI
https://dx.doi.org/10.17504/protocols.io.4r3l24zq3g1y/v1
  • Dakota Betz1
  • 1ucsd
  • Rouse Lab
Dakota Betz
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DOI: https://dx.doi.org/10.17504/protocols.io.4r3l24zq3g1y/v1
Protocol Citation: Dakota Betz 2025. Mitogenome Assembly with GetOrganelle. protocols.io https://dx.doi.org/10.17504/protocols.io.4r3l24zq3g1y/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: July 09, 2021
Last Modified: June 18, 2025
Protocol Integer ID: 51443
Keywords: mitogenome assembly with getorganelle basic instruction, assembling mitogenome, mitogenome assembly, getorganelle basic instruction, instruction
Abstract
Basic instructions for assembling mitogenomes with the GetOrganelle Program
Troubleshooting
Installation

Note
This protocol includes instructions for a conda install of GetOrganelle, which requires that you have Anaconda or Miniconda already installed on your system.

Detailed installation information and additional installation options for various systems can be found here: https://github.com/Kinggerm/GetOrganelle
and here: https://github.com/Kinggerm/GetOrganelle/wikihttps://github.com/Kinggerm/GetOrganelle/wiki

Before installation, activate your python environment (example code below for python3 environment):

Command
new command name
conda activate python3

Install GetOrganelle with the following code:

Command
new command name
conda install -c bioconda getorganelle

You may need to install updates, be sure to say yes (type y and hit enter) when prompted to update any conda-related programs.

Printout of successful installation of GetOrganelle (for reference).

Initialization
Next we need to download and initialize the database of your preferred organelle genome type.
Options include: embplant_pt, embplant_mt, embplant_nr, fungus_mt, fungus_nr, animal_mt, and/or other_pt

For animal mitochondrial genomes, use animal_mt:

Command
new command name
get_organelle_config.py --add animal_mt
If you would like to download and initialize multiple organelle genome types, you can list them after the --add command above, separated by spaces.

Printout of successful initialization (for reference). Note that working directories will be different on your system.

If you have trouble with the above command (connection to GitHub fails) try a few times more, as the problem generally resolves itself. If you're still having trouble, you can download the repository manually, as in Option 2 available here: https://github.com/Kinggerm/GetOrganelle/wiki/Initialization#default-directory