recipe longqc

LongQC is a tool for the data quality control of the PacBio and ONT long reads






package longqc

(downloads) docker_longqc



depends h5py:

depends jinja2:

depends matplotlib-base:


depends minimap2-coverage:

depends numpy:

depends pandas:


depends pysam:

depends python:


depends python-edlib:

depends scikit-learn:

depends scipy:



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 longqc

and update with::

   mamba update longqc

To create a new environment, run:

mamba create --name myenvname longqc

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

Download stats