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metaT_pipe

pipelines

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 Installation for software that require databases

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

Usage

  • Get help with the following command
PATH_TO_META_PIPE/metaT_pipe.py -h

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Scripts for running metatranscriptomic analysis

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