Metatranscriptomics is an exciting new area of inquiry with important applications in medical and environmental science fields, among others. By analyzing the RNA of a biological community--perhaps that of an organism's microbiome or free-living marine microbes--we can determine which genes are actually being expressed by the community, and, therefore, which functions the organisms in that community are actively carrying out.
Conda Dependencies: environment.yml
Pip Dependencies: requirements.txt
The MarMMA pipline can be installed using the conda and pip dependecy lists. While in the root directory execute the following
apt-get install -y make zlib1g-dev gcc g++ python3-pip
conda env create -f environment.yml --force
pip install -r requirements.txt --no-cache-dir
-i : Input file path
-kdb : Path to kraken2 database
--run-kraken : Execute the kraken2 contamination removal
** By default kraken2 is skipped
Use -h so see full usage