recipe straglr

Short-tandem repeat genotyping using long reads



GPL3 / GPL-3.0-or-later




doi: 10.1186/s13059-021-02447-3

package straglr

(downloads) docker_straglr



depends blast:

depends intspan:


depends numpy:


depends pathos:


depends pybedtools:


depends pysam:


depends python:


depends scikit-learn:


depends scipy:


depends trf:



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 straglr

and update with::

   mamba update straglr

To create a new environment, run:

mamba create --name myenvname straglr

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

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