recipe mitofinder

Mitofinder is a pipeline to assemble mitochondrial genomes and annotate mitochondrial genes from trimmed read sequencing data.






package mitofinder

(downloads) docker_mitofinder



depends biopython:

depends blast:

depends idba:

depends libgcc-ng:


depends megahit:

depends openjdk:

depends pandas:

depends python:


depends python_abi:

2.7.* *_cp27mu

depends spades:

depends trnascan-se:



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 mitofinder

and update with::

   mamba update mitofinder

To create a new environment, run:

mamba create --name myenvname mitofinder

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 `mitofinder/tags`_ for valid values for ``<tag>``)

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