- recipe kneaddata
KneadData is a tool designed to perform quality control on metagenomic sequencing data.
- Homepage:
- Developer docs:
- License:
MIT / MIT
- Recipe:
KneadData is a tool designed to perform quality control on metagenomic sequencing data, especially data from microbiome experiments. In these experiments, samples are typically taken from a host in hopes of learning something about the microbial community on the host. However, metagenomic sequencing data from such experiments will often contain a high ratio of host to bacterial reads. This tool aims to perform principled in silico separation of bacterial reads from these "contaminant" reads, be they from the host, from bacterial 16S sequences, or other user-defined sources.
- package kneaddata¶
- Versions:
0.12.4-0,0.12.3-0,0.12.2-0,0.12.1-0,0.12.0-1,0.12.0-0,0.10.0-0,0.9.0-0,0.7.4-1,0.12.4-0,0.12.3-0,0.12.2-0,0.12.1-0,0.12.0-1,0.12.0-0,0.10.0-0,0.9.0-0,0.7.4-1,0.7.4-0,0.7.3-0,0.7.2-1,0.7.2-0,0.7.0-0,0.6.1-2,0.6.1-0,0.5.2-0- Depends:
on blast
on bmtool
on bowtie2
>=2.2on fastqc
on python
>=3on samtools
on srprism
on trf
on trimmomatic
- Additional platforms:
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 kneaddata
to add into an existing workspace instead, run:
pixi add kneaddata
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 kneaddata
Alternatively, to install into a new environment, run:
conda create -n envname kneaddata
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/kneaddata:<tag>
(see kneaddata/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/kneaddata/README.html)
