KneadData is a tool designed to perform quality control on metagenomic sequencing data, especially data from microbiome experiments. 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.
We provide support for KneadData users. Please report any issues on the KneadData Issues page.
KneadData can be installed with Homebrew or run from a Docker image. Please note, if you are using bioBakery (Vagrant VM or Google Cloud) you do not need to install KneadData because the tool and its dependencies are already installed.
Install with Homebrew: $ brew install biobakery/biobakery/kneaddata
Install with Docker: $ docker run -it biobakery/kneaddata bash
If you would like to install from source, refer to the KneadData user manual for the pre-requisites/dependencies and installation instructions.
Under construction: Check back soon for more updates!