kneaddata¶
Description¶
KneadData is a tool designed to perform quality control on metagenomic and metatranscriptomic 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, 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. Additionally, KneadData can be used for other filtering tasks. For example, if one is trying to clean data derived from a human sequencing experiment, KneadData can be used to separate the human and the non-human reads.
Environment Modules¶
Run module spider kneaddata to find out what environment modules are available for this application.
Environment Variables¶
- HPC_KNEADATA_DIR - installation directory
- HPC_KNEADATA_BIN - executable directory
Categories¶
phylogenetics