recipe basic

BASIC is a semi-de novo assembly method for assembling BCR and TCR genes from single cell RNA-seq data.






package basic

(downloads) docker_basic



depends bowtie2:

depends python:



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 basic

and update with::

   mamba update basic

To create a new environment, run:

mamba create --name myenvname basic

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

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