recipe megalodon

Nanopore modified base and sequence variant detection.




OTHER / Oxford Nanopore Technologies PLC. Public License Version 1.0



package megalodon

(downloads) docker_megalodon



depends h5py:


depends libgcc-ng:


depends mappy:


depends numpy:


depends numpy:


depends ont-fast5-api:


depends pysam:


depends python:


depends python_abi:

3.10.* *_cp310

depends scikit-learn:

depends scipy:


depends seaborn:

depends tqdm:




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 megalodon

and update with::

   mamba update megalodon

To create a new environment, run:

mamba create --name myenvname megalodon

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

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