recipe pavfinder

PAVFinder is a Python package that detects structural variants from de novo assemblies.







doi: 10.1186/s12920-018-0402-6, doi: 10.1093/bioinformatics/btz902

package pavfinder

(downloads) docker_pavfinder



depends bash:

depends biobloomtools:

depends biopython:

depends blast:

depends bwa:

depends gmap:

depends intspan:


depends make:

depends pybedtools:


depends pysam:


depends python:


depends rnabloom:

depends ruffus:

depends samtools:

depends transabyss:



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 pavfinder

and update with::

   mamba update pavfinder

To create a new environment, run:

mamba create --name myenvname pavfinder

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

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