recipe pathogen-profiler

Library giving access to classes and functions to create a profiling tool to look for mutations from NGS data.






package pathogen-profiler

(downloads) docker_pathogen-profiler



depends bcftools:


depends bedtools:

depends bwa:

depends delly:


depends dsk:


depends freebayes:


depends gatk4:

depends git:

depends itol-config:

depends joblib:


depends kmc:


depends lofreq:


depends minimap2:

depends openjdk:


depends parallel:

depends pilon:


depends pydantic:


depends pysam:

depends python:


depends requests:

depends rich-argparse:

depends samclip:

depends samtools:


depends seqkit:

depends snpeff:


depends sourmash:

depends tomli:

depends tqdm:

depends trimmomatic:



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 pathogen-profiler

and update with::

   mamba update pathogen-profiler

To create a new environment, run:

mamba create --name myenvname pathogen-profiler

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 `pathogen-profiler/tags`_ for valid values for ``<tag>``)

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