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.
KneadData is available as a bitbucket repository.
We provide support for KneadData users. Please report any issues on the KneadData Issues page.
KneadData Tutorial HERE