Mag Docker Image

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 [***] 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 https://nf-co.re/usage/installation

2. Install any of https://docs.docker.com/engine/installation/, https://www.sylabs.io/guides/3.0/user-guide/ or https://podman.io/ for full pipeline reproducibility (please only use https://conda.io/miniconda.html as a last resort; see https://nf-co.re/usage/configuration#basic-configuration-profiles)

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

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

   Please check https://github.com/nf-core/configs#documentation 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!

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

See https://nf-co.re/mag/usage and https://nf-co.re/mag/parameters 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 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://github.com/DerrickWood/kraken2/wiki
• performs assembly using https://github.com/voutcn/megahit and 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 Busco
• assigns taxonomy to bins using https://github.com/dutilh/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: https://nf-co.re/mag/usage and https://nf-co.re/mag/output. Detailed information about how to specify the input can be found under https://nf-co.re/mag/usage#input_specifications.

Group-wise co-assembly and co-abundance computation

Each sample has an associated group ID (see https://nf-co.re/mag/usage#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 https://nf-co.re/mag/parameters#coassemble_group and https://nf-co.re/mag/parameters#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, https://github.com/d4straub and https://github.com/skrakau at the Quantitative Biology Center (QBiC).

Long read processing was inspired by https://github.com/caspargross/HybridAssembly written by Caspar Gross https://github.com/caspargross

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

• https://github.com/apeltzer
• https://github.com/ewels
• https://github.com/ggabernet
• https://github.com/drpatelh
• https://github.com/alneberg
• https://github.com/maxibor
• https://github.com/MaxUlysse
• https://github.com/heuermh

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 https://nf-co.re/join/slack).

Citations

If you use nf-core/mag for your analysis, please cite it using the following doi: https://doi.org/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: https://dx.doi.org/10.1038/s41587-020-0439-x. ReadCube: Full Access Link