recipe getorganelle

Get organelle genomes from genome skimming data




GPL3 / GPL-3.0-or-later




doi: 10.1186/s13059-020-02154-5, biotools: getorganelle, usegalaxy-eu: get_organelle_from_reads, usegalaxy-eu: get_annotated_regions_from_gb

package getorganelle

(downloads) docker_getorganelle


depends blast:


depends bowtie2:


depends numpy:


depends perl:

depends pigz:

depends python:


depends requests:

depends scipy:


depends spades:


depends sympy:


depends tbb:




You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install getorganelle

and update with::

   mamba update getorganelle

To create a new environment, run:

mamba create --name myenvname getorganelle

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

(see `getorganelle/tags`_ for valid values for ``<tag>``)

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