recipe aquamis

AQUAMIS is a snakemake pipeline for routine assembly and quality assessment of microbial isolate sequencing experiments.






package aquamis

(downloads) docker_aquamis



depends bbmap:


depends biopython:


depends blast:


depends bracken:


depends bwa:


depends cerberus:


depends circos:


depends confindr:


depends entrez-direct:


depends fastp:


depends genson:


depends jsonschema:


depends kma:


depends kmc:


depends kraken2:


depends mash:


depends minimap2:


depends mlst:


depends numpy:


depends pandas:


depends pandoc:


depends perl-bio-tools-run-alignment-tcoffee:

1.7.4 pl5321hdfd78af_4

depends pilon:


depends python:


depends pyyaml:


depends quast:


depends r-base:


depends r-dt:


depends r-knitr:


depends r-rmarkdown:


depends r-rrapply:


depends r-tidyverse:


depends r-urltools:


depends samtools:


depends seqtk:


depends shovill:


depends snakemake-minimal:


depends spades:


depends taxonkit:


depends trimmomatic:


depends tzdata:



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 aquamis

and update with::

   mamba update aquamis

To create a new environment, run:

mamba create --name myenvname aquamis

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

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