This pipeline is for assembly, binning, and annotation of metagenomes.

nf-core/mag workflow overview

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.

Quick Start

  1. Install nextflow

  2. Install any of Docker, Singularity or Podman for full pipeline reproducibility (please only use Conda as a last resort; see docs)

  3. Download the pipeline and test it on a minimal dataset with a single command:

    nextflow run nf-core/mag -profile test,<docker/singularity/podman/conda/institute>

    Please check nf-core/configs to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use -profile <institute> in your command. This will enable either docker or singularity and set the appropriate execution settings for your local compute environment.

  4. Start running your own analysis!

    nextflow run nf-core/mag -profile <docker/singularity/podman/conda/institute> --input '*_R{1,2}.fastq.gz'

See usage docs for all of the available options when running the pipeline.


The nf-core/mag pipeline comes with documentation about the pipeline: usage and output.

In short, it supports both short and long reads, quality trims the reads and adapters with fastp and porechop, and performs basic QC with fastqc. The pipeline then:

  • assigns taxonomy to reads using centrifuge and/or kraken2
  • performs assembly using megahit and spades, and checks their quality using quast
  • performs metagenome binning using metabat2, and checks the quality of the genome bins using busco
  • assigns taxonomy to bins using CAT

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


nf-core/mag was written by Hadrien Gourlé at SLU, Daniel Straub and Sabrina Krakau at the Quantitative Biology Center (QBiC).

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

Many thanks to the additional contributors who have helped out and/or provided suggestions:

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

For further information or help, don’t hesitate to get in touch on the Slack #mag channel (you can join with this invite).


If you use nf-core/mag for your analysis, please cite it using the following doi: 10.5281/zenodo.3589527

You can cite the nf-core publication as follows:

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x. ReadCube: Full Access Link