Scripts for running metatranscriptomic analysis
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
- 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
For CheckM download the required database reference data following the instructions from CheckM website.
For DRAM follow the instructions for DRAM septup
For GDTB-Tk run the following
download-db.sh
For Dirseq installation
gem install dirseq
- Get help with the following command
PATH_TO_META_PIPE/metaT_pipe.py -h