recipe milonga

MiLongA - A snakemake workflow for Microbial Long-read Assembly






package milonga

(downloads) docker_milonga



depends abricate:


depends bcftools:


depends bedtools:


depends bioawk:


depends bioconductor-biocgenerics:

depends bioconductor-biostrings:

depends bioconductor-iranges:

depends biopython:


depends blast:


depends bowtie2:


depends checkm-genome:


depends diamond:


depends flye:


depends kraken2:


depends miniasm:


depends minimap2:


depends mummer4:


depends nanofilt:


depends nanostat:


depends pandas:


depends pilon:


depends pip:


depends platon:


depends porechop:


depends prodigal:


depends qcat:


depends r-base:

depends r-dplyr:

depends r-dt:

depends r-ggplot2:

depends r-knitr:

depends r-optparse:

depends r-plotly:

depends r-rmarkdown:

depends r-tidyr:

depends racon:


depends samtools:


depends snakemake-minimal:


depends spades:


depends taxonkit:


depends unicycler:


depends yaml:




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 milonga

and update with::

   mamba update milonga

To create a new environment, run:

mamba create --name myenvname milonga

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

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