recipe aquila

Diploid personal genome assembly and comprehensive variant detection based on linked-reads






package aquila

(downloads) docker_aquila



depends minimap2:

depends numpy:

depends pysam:


depends python:


depends samtools:

depends scipy:



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 aquila

and update with::

   mamba update aquila

To create a new environment, run:

mamba create --name myenvname aquila

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

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