A workflow for metagenomic projects
This is a snakemake workflow that processes paired-end and/or single-end metagenomic samples.
Potential analyses include:
- read-based taxonomic classification
- functional and taxonomic annotation of coding sequences
- genome binning of assembled contigs
Clone the repository
Checkout the latest version of this repository (to your current directory):
git clone https://bitbucket.org/scilifelab-lts/lts-workflows-sm-metagenomics
Install the required software
All the software needed to run this workflow is included as a conda environment file.
To create the environment
sm-meta use the supplied environment.yaml file
found in the lts_workflows_sm_metagenomics/envs/ folder.
conda env create -f lts_workflows_sm_metagenomics/envs/environment.yaml
Optional: To install the software environment inside the workflow directory (instead of in your home directory) you can run:
conda env create -p envs/sm-meta -f envs/environment.yaml
This creates the
sm-meta environment inside the
envs/ directory and
installs the environment there.
Next, add this directory to the envs_dirs in your conda config (this is to simplify activation of the environment and so that the full path of the environment installation isn't shown in your bash prompt):
conda config --add envs_dirs <full_path_to_repository>/envs/
Activate the environment using:
conda activate sm-meta
(Optional) Install mapdamage
If you plan on running analyses using mapdamage to
identify 'ancient' sequences in your data you should also install the
mapdamage conda environment:
conda env create -f lts_workflows_sm_metagenomics/envs/mapdamage.yaml
See the documentation for instructions on how to run the pipeline.