nf-core/mag

Edit

Introduction

This pipeline is for assembly, binning and annotation of metagenomes. It supports both short and long reads, quality trims the reads and adapters with https://github.com/OpenGene/fastp and https://github.com/rrwick/Porechop and performs basic QC with https://www.bioinformatics.babraham.ac.uk/projects/fastqc/.

The pipeline then:

• assigns taxonomy to reads using https://ccb.jhu.edu/software/centrifuge/ and/or https://ccb.jhu.edu/software/kraken2/
• performs assembly using https://github.com/voutcn/megahit and http://cab.spbu.ru/software/spades/, and checks their quality using http://quast.sourceforge.net/quast
• performs metagenome binning using https://bitbucket.org/berkeleylab/metabat/src/master/, and checks the quality of the genome bins using https://busco.ezlab.org/

Furthermore, the pipeline creates various reports in the results directory specified, including a https://multiqc.info/ 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.

Documentation

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

1. Installation
2. Pipeline configuration
   • Local installation
   • Adding your own system config
   • Reference genomes
3. Running the pipeline
4. Output and how to interpret the results
5. Troubleshooting

Credits

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