Note: Looking for the original CompareM (AAI and codon usage)? See github.com/donovan-h-parks/CompareM.
CompareM2 is a genomes-to-report pipeline for comparative analysis of bacterial and archaeal genomes. It takes genome assemblies — isolates or MAGs — and runs 30+ analysis tools, producing a portable HTML report with publication-ready graphics.
- 30+ integrated analyses — quality control, annotation, functional annotation, phylogenetics, pan/core genomes, AMR profiling, metabolic modeling, and more. Full list.
- Dynamic HTML report — collects central results into a single portable file with interpretable figures and text. Adapts to partial runs — only includes sections for completed analyses. See examples.
- Assembly-agnostic — works strictly downstream of assembly and binning. Accepts genomes from any sequencing technology or source.
- Scalable — runs on local workstations (recommended >= 64 GiB RAM) or HPC clusters (SLURM/PBS). Scales approximately linearly with input size thanks to Snakemake's parallel job scheduling.
- Easy to install — single command via pixi or mamba. All dependencies are managed via conda environments or a pre-built Docker/Apptainer image.
- Configurable — passthrough arguments forward any parameter to any underlying tool. Add NCBI reference genomes by accession.
# Install
pixi global install -c conda-forge -c bioconda comparem2
# Run fast analyses on your genomes
comparem2 --config input_genomes="*.fna" --until fast
# Run the full pipeline
comparem2See the documentation for installation options, usage details, and the full list of analyses.
Kobel C.M., Aho V.T.E., Øyås O., Nørskov-Lauritsen N., Woodcroft B.J., Pope P.B. CompareM2 is a genomes-to-report pipeline for comparing microbial genomes. Bioinformatics 41(9), btaf517 (2025). doi:10.1093/bioinformatics/btaf517
- Documentation: comparem2.readthedocs.io
- Issues and questions: github.com/cmkobel/CompareM2/issues