NBIS Metagenomics Workflow



This is a snakemake workflow for preprocessing and analysis of metagenomic datasets. It can handle single- and paired-end data and can run on a local laptop with either Linux or OSX, or in a cluster environment.

The source code is available at GitHub and is being developed as part of the NBIS bioinformatics infrastructure.


1. Clone the repository Checkout the latest version of this repository (to your current directory):

git clone git@github.com:NBISweden/nbis-meta.git
cd nbis-meta

Change directory:

cd nbis-meta

2. Install the required software All the software needed to run this workflow is included as a Conda environment file. See the conda installation instructions for how to install conda on your system.

To create the environment nbis-meta use the supplied environment.yaml file:

mkdir envs/nbis-meta
conda env create -f environment.yaml -p envs/nbis-meta

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 $(pwd)/envs/

Activate the environment using:

conda activate envs/nbis-meta

You are now ready to start using the workflow!


If you plan on using the workflow in a cluster environment running the SLURM workload manager (such as Uppmax) you should configure the workflow with the SLURM snakemake profile. See the documentation.