CompareM2

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.

<a href="https://comparem2.readthedocs.io/en/latest/30%20what%20analyses%20does%20it%20do/#rendered-report"><img width="220" style="width: 220px" alt="report document logo" align="right" src="https://github.com/cmkobel/comparem2/assets/5913696/e5f9b72c-2137-4850-8779-a5528d8ccbaf"></a>

Features

• 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.

Quick start

# 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
comparem2

See the documentation for installation options, usage details, and the full list of analyses.

Citation

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

Links

• Documentation: comparem2.readthedocs.io
• Issues and questions: github.com/cmkobel/CompareM2/issues