recipe plasmidid

Pipeline for plasmid identification and reconstruction






PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification.

package plasmidid

(downloads) docker_plasmidid



depends bc:

depends bedtools:

depends biopython:

depends blast:

depends bowtie2:

depends circos:

depends gawk:

depends mash:


depends numpy:

depends pandas:

depends perl-gd:


depends prokka:


depends python:


depends samtools:

depends scikit-learn:

depends scipy:

depends spades:

depends tabulate:

depends tbb:


depends trimmomatic:

depends wget:



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 plasmidid

and update with::

   mamba update plasmidid

To create a new environment, run:

mamba create --name myenvname plasmidid

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

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