recipe kneaddata

KneadData is a tool designed to perform quality control on metagenomic sequencing data.






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

(downloads) docker_kneaddata



depends blast:

depends bmtool:

depends bowtie2:


depends fastqc:

depends python:


depends samtools:

depends srprism:

depends trf:

depends trimmomatic:



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 kneaddata

and update with::

   mamba update kneaddata

To create a new environment, run:

mamba create --name myenvname kneaddata

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

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