recipe crispresso

A software pipeline for the analysis of targeted CRISPR-Cas9 sequencing data






package crispresso

(downloads) docker_crispresso



depends argparse:

depends biopython:


depends bowtie2:

depends emboss:

depends flash:

depends libgcc-ng:


depends matplotlib:


depends mock:

depends nose:

depends numpy:


depends openjdk:


depends pandas:


depends python:


depends python_abi:

2.7.* *_cp27mu

depends samtools:

depends seaborn:

depends trimmomatic:



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 crispresso

and update with::

   mamba update crispresso

To create a new environment, run:

mamba create --name myenvname crispresso

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

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