MAGmaker¶
A Snakemake pipeline for end-to-end processing of metagenomic shotgun sequencing data (paired-end or single-end). MAGmaker takes raw FASTQ files through quality control, host read removal, assembly, and taxonomic profiling, then — in a second stage — through mapping, binning, bin consolidation, and MAG QC to produce metagenome-assembled genomes (MAGs). An optional viral / plasmid discovery track (geNomad + CheckV) runs alongside the MAG track.
Developed by the Moeller Lab at Cornell University and Princeton University, and maintained by the Sprockett Lab at Wake Forest University School of Medicine.
Quick start¶
git clone https://github.com/SprockettLab/MAGmaker.git
cd MAGmaker
mamba env create -n snakemake -f resources/env/snakemake.yaml
conda activate snakemake
# Edit resources/config/config.yaml and metadata.txt
# Run Stage 1 + Stage 2 through MAG renaming
./run_magmaker.sh --cores 8 --use-conda
# On an HPC cluster with a Snakemake SLURM profile
./run_magmaker.sh --profile resources/profiles/your_cluster
WFUSM users on DEMON: start at Running on DEMON — all databases and environments are pre-configured.
Where to go next¶
| Page | Contents |
|---|---|
| Pipeline overview | What each stage does and why, tool choices, the two-Snakefile structure |
| Installation | Requirements, conda setup, test data |
| Configuration | config.yaml, metadata.txt, binning.txt |
| Database setup | CheckM2, GUNC, GTDB-Tk, MetaPhlAn, Kraken2, geNomad, CheckV, host genome |
| Running the pipeline | Local, HPC/SLURM, run_magmaker.sh, per-run flags, stage-by-stage |
| Output | Directory layout, MAG summary table, renaming workflow, GTDB-Tk stages |
| Viral / plasmid track | geNomad + CheckV, virus_summary.tsv |
| Running on DEMON (WFUSM) | DEMON cluster setup, pre-configured databases and environments |
Citation¶
Sanders JG, Sprockett DD, Li Y, Mjungu D, Lonsdorf EV, Ndjango JN, Georgiev AV, Hart JA, Sanz CM, Morgan DB, Peeters M, Hahn BH, Moeller AH. Widespread extinctions of co-diversified primate gut bacterial symbionts from humans. Nat Microbiol. 2023 Jun;8(6):1039-1050. doi: 10.1038/s41564-023-01388-w. PMID: 37169918.