recipe winnowmap

Winnowmap is a long-read mapping algorithm optimized for mapping ONT and PacBio reads to repetitive reference sequences.



LicenseRef-Public-Domain AND MIT




doi: 10.1093/bioinformatics/btaa435

package winnowmap

(downloads) docker_winnowmap



depends _openmp_mutex:


depends libgcc-ng:


depends libstdcxx-ng:


depends libzlib:


depends meryl:




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 winnowmap

and update with::

   mamba update winnowmap

To create a new environment, run:

mamba create --name myenvname winnowmap

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

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