# NBIS Metagenomics Workflow¶

Preprocessing

## Overview¶

This is a snakemake workflow for rocessing 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 BitBucket and is being developed as part of the NBIS bioinformatics infrastructure.

## Installation¶

git clone https://bitbucket.org/scilifelab-lts/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 envs/environment.yaml file:

mkdir envs/nbis-meta
conda env create -f envs/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!

Note

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.