Assembly, binning and annotation of metagenomes.

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