recipe asqcan

A combined pipeline for bacterial genome assembly, quality control and annotation



GPL / GPL-3.0-only



package asqcan

(downloads) docker_asqcan



depends blast:

depends blobtools:

depends bwa:

depends diamond:

depends fastp:

depends parallel:

depends prokka:

depends python:

depends quast:

depends requests:

depends samtools:

depends spades:



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 asqcan

and update with::

   mamba update asqcan

To create a new environment, run:

mamba create --name myenvname asqcan

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

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