recipe harpy

Process raw haplotagging data, from raw sequences to phased haplotypes.



Developer docs:


GPL3 / GPL-3.0-or-later



Harpy is a command-line tool to easily process haplotag or 10x linked-read data. It uses Snakemake under the hood to execute different workflows (quality control, trimming, alignment, variant calling, phasing, etc.), but the user is rarely, if ever, exposed to Snakemake directly. With an emphasis on user-friendliness, parallelization, transparency, and reproducibility, Harpy aims to quickly handle data processing so that you can focus more on analyzing your data.

package harpy

(downloads) docker_harpy



depends apptainer:

depends bcftools:


depends libgcc-ng:


depends libstdcxx-ng:


depends pandas:

depends pysam:

depends python:


depends python_abi:

3.12.* *_cp312

depends rich-click:

depends samtools:


depends seqtk:

depends snakemake-minimal:


depends tabix:



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 harpy

and update with::

   mamba update harpy

To create a new environment, run:

mamba create --name myenvname harpy

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

Download stats