recipe crabs

Crabs (Creating Reference databases for Amplicon-Based Sequencing) is a program to download and curate reference databases for eDNA metabarcoding analyses



MIT License



package crabs

(downloads) docker_crabs



depends argparse:

depends biopython:


depends cutadapt:


depends matplotlib-base:

depends muscle:


depends numpy:

depends pandas:


depends python:


depends tqdm:

depends vsearch:


depends wget:



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 crabs

and update with::

   mamba update crabs

To create a new environment, run:

mamba create --name myenvname crabs

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

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