recipe smeg

Strain-level Metagenomic Estimation of Growth rate (SMEG) measures growth rates of microbial strains from complex metagenomic dataset






package smeg

(downloads) docker_smeg



depends bamtools:

depends bedtools:

depends blast:

depends bowtie2:

depends libgenome:

depends mauve:

depends openssl:


depends parallel:

depends prokka:

depends r-ape:

depends r-data.table:

depends r-dplyr:

depends r-dynamictreecut:

depends r-getopt:

depends r-ggplot2:

depends r-gplots:

depends r-gsubfn:

depends r-seqinr:

depends readline:


depends roary:

depends samtools:



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 smeg

and update with::

   mamba update smeg

To create a new environment, run:

mamba create --name myenvname smeg

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

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