This pipeline is for assembly, binning and annotation of metagenomes. It supports both short and long reads, quality trims the reads and adapters with and and performs basic QC with

The pipeline then:

Furthermore, the pipeline creates various reports in the results directory specified, including a report summarizing some of the findings and software versions.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.


The nf-core/mag pipeline comes with documentation about the pipeline, found in the docs/ directory:

  1. Installation
  2. Pipeline configuration
  3. Running the pipeline
  4. Output and how to interpret the results
  5. Troubleshooting


This pipeline was written by Hadrien Gourlé at SLU and Daniel Straub (@d4straub).

Long read processing was inspired by caspargross/HybridAssembly written by Caspar Gross @caspargross