recipe quantpi

A general profiling system focus on robust microbiome research



GPL / GPL-3.0-only




biotools: quantpi

package quantpi

(downloads) docker_quantpi



depends bedtools:

depends biopython:

depends bowtie2:

depends bracken:


depends bwa:

depends coverm:


depends fastp:

depends fastqc:

depends humann:

depends kmcp:


depends kraken2:

depends krakentools:


depends krona:

depends matplotlib-base:

depends metaphlan:

depends multiqc:

depends natsort:

depends numpy:

depends openpyxl:

depends pandas:

depends pigz:

depends python:

depends ruamel.yaml:

depends sambamba:

depends samtools:

depends seaborn:

depends seqkit:

depends snakemake:



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 quantpi

and update with::

   mamba update quantpi

To create a new environment, run:

mamba create --name myenvname quantpi

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

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