- recipe kmc
Tools for efficient k-mer counting and filtering of reads based on k-mer content.
- Homepage:
- Documentation:
- License:
GPL3 / GPL-3.0-or-later
- Recipe:
- Links:
biotools: kmc, doi: 10.1093/bioinformatics/btx304, doi: 10.1093/bioinformatics/btv022, doi: 10.1186/1471-2105-14-160
KMC is a utility designed for counting k-mers (sequences of consecutive k symbols) in a set of DNA sequences. KMC tools allow performing various operations on k-mers sets.
- package kmc¶
- Versions:
3.2.4-5,3.2.4-4,3.2.4-3,3.2.4-2,3.2.4-1,3.2.4-0,3.2.1-3,3.2.1-2,3.2.1-1,3.2.4-5,3.2.4-4,3.2.4-3,3.2.4-2,3.2.4-1,3.2.4-0,3.2.1-3,3.2.1-2,3.2.1-1,3.2.1-0,3.1.2rc1-0,3.1.1-1,3.1.1-0,3.1.1rc1-2,3.1.1rc1-1,3.1.1rc1-0,3.1.0-0,3.0.1-2,3.0.1-1,3.0.1-0,3.0.0-3,3.0.0-2,3.0.0-1,3.0.0-0,2.3.0-3,2.3.0-2,2.3.0-1- Depends:
on libgcc
>=13on libstdcxx
>=13on libzlib
>=1.3.1,<2.0a0on python
>=3
- Additional platforms:
linux-aarch64,osx-arm64
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install kmc
to add into an existing workspace instead, run:
pixi add kmc
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install kmc
Alternatively, to install into a new environment, run:
conda create -n envname kmc
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/kmc:<tag>
(see kmc/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/kmc/README.html)
