metaT_pipe

Scripts for running metatranscriptomic analysis

Dependencies

The following software is required to run this pipeline:

• dRep pipeline used to "de-replicate" genomes
• cd-hit "de-replication" of contigs using clustering
• DRAM metagenomic assembled genomes annotation
• CheckM quality control of metagenomes
• GTDB-Tk taxonomic assignment
• CoverM reads mapping
• dirseq gene counts

Installation

• Clone the repository in your home directory and make the script executable

git clone https://github.com/Coayala/metaT_pipe.git
cd metaT_pipe
chmod +x metaT_pipe.py

• Create and activate environment

conda env create -f environment.yml
conda activate metaT_pipe

-Finish DRAM and GDTB-Tk installation For DRAM follow the instructions for DRAM septup

For GDTB-Tk run the following

download-db.sh

Usage

-Get help with the following command

PATH_TO_META_PIPE/metaT_pipe.py -h