Mag

Assembly and binning of metagenomes

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Install / Use

npx skills add nf-core/mag

Installs into whichever agent you are using.

About this skill

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README

Introduction

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

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, AdapterRemoval, or trimmomatic and Porechop, and performs basic QC with FastQC, and merges multiple sequencing runs.

The pipeline then:

performs assembly using MEGAHIT and SPAdes, and checks their quality using Quast and ALE (if short read data is used)
(optionally) polishes long-read assemblies with short reads using pypolca
(optionally) performs ancient DNA assembly validation using PyDamage and contig consensus sequence recalling with Freebayes and BCFtools
predicts protein-coding genes for the assemblies using Prodigal, and bins with Prokka and optionally MetaEuk
performs metagenome binning using MetaBAT2, MaxBin2, CONCOCT, COMEBin, MetaBinner, and/or SemiBin2
checks the quality of the genome bins using Busco, CheckM, or CheckM2 and optionally GUNC
Performs ancient DNA validation and repair with pyDamage and freebayes
optionally refines bins with DAS Tool
assigns taxonomy to bins using GTDB-Tk and/or CAT and optionally identifies viruses in assemblies using geNomad, or Eukaryotes with Tiara

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

Usage

[!NOTE] If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

nextflow run nf-core/mag -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> --input samplesheet.csv --outdir <OUTDIR>

[!WARNING] Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

For more details and further functionality, please refer to the usage documentation and the parameter documentation.

Pipeline output

To see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the output documentation.

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.