- recipe coverm
CoverM aims to be a configurable, easy to use and fast DNA read coverage and relative abundance calculator focused on metagenomics applications
- Homepage:
- License:
GPL3 / GPL3
- Recipe:
- package coverm¶
- versions:
0.7.0-2,0.7.0-1,0.7.0-0,0.6.1-6,0.6.1-5,0.6.1-4,0.6.1-3,0.6.1-2,0.6.1-1,0.7.0-2,0.7.0-1,0.7.0-0,0.6.1-6,0.6.1-5,0.6.1-4,0.6.1-3,0.6.1-2,0.6.1-1,0.6.1-0,0.6.0-0,0.5.0-0,0.4.0-2,0.4.0-1,0.4.0-0,0.3.2-0,0.3.1-0,0.3.0-0,0.2.0.alpha7-0- depends bwa:
>=0.7.17- depends dashing:
>=0.4.0- depends fastani:
>=1.31- depends gsl:
>=2.7,<2.8.0a0- depends libgcc:
>=13- depends libstdcxx:
>=13- depends libzlib:
>=1.3.1,<2.0a0- depends minimap2:
>=2.24- depends openblas:
- depends samtools:
>=1.9- depends starcode:
- depends strobealign:
>=0.11.0- depends zlib:
- requirements:
- additional platforms:
Installation
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 coverm and update with:: mamba update coverm
To create a new environment, run:
mamba create --name myenvname coverm
with
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).Alternatively, use the docker container:
docker pull quay.io/biocontainers/coverm:<tag> (see `coverm/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/coverm/README.html)
