nfcore/mag repository overview

Assembly, binning and annotation of metagenomes.

⁠Introduction

nf-core/mag is a bioinformatics best-practise analysis pipeline for assembly, binning, and annotation of metagenomes.

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>
   

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   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'
   

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

⁠Pipeline Summary

By default, the pipeline currently performs the following: 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.

⁠Documentation

The nf-core/mag pipeline comes with documentation about the pipeline: usage⁠ and output⁠. Detailed information about how to specify the input can be found under input specifications⁠.

⁠Group-wise co-assembly and co-abundance computation

Each sample has an associated group ID (see input specifications⁠). This group information can be used for group-wise co-assembly with MEGAHIT or SPAdes and/or to compute co-abundances for the binning step with MetaBAT2. By default, group-wise co-assembly is disabled, while the computation of group-wise co-abundances is enabled. For more information about how this group information can be used see the documentation for the parameters --coassemble_group⁠ and --binning_map_mode⁠.

When group-wise co-assembly is enabled, SPAdes is run on accordingly pooled read files, since metaSPAdes does not yet allow the input of multiple samples or libraries. In contrast, MEGAHIT is run for each group while supplying lists of the individual readfiles.

⁠Credits

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:

• Alexander Peltzer⁠
• Phil Ewels⁠
• Gisela Gabernet⁠
• Harshil Patel⁠
• Johannes Alneberg⁠
• Maxime Borry⁠
• Maxime Garcia⁠
• Michael L Heuer⁠

⁠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).

⁠Citations

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: