recipe pbhoover

Variant caller for legacy and low coverage Pacific Biosciences' long-read sequencing data






package pbhoover

(downloads) docker_pbhoover



depends bcftools:


depends htslib:


depends pbcore:


depends pbh5tools:


depends python:


depends pyvcf:




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 pbhoover

and update with::

   mamba update pbhoover

To create a new environment, run:

mamba create --name myenvname pbhoover

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

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