!!! note If you're looking for the original version of CompareM, a tool to calculate AAI and codon usage, please follow this link: github.com/donovan-h-parks/CompareM
🧬 CompareM2 is a "pre-plumbed", scalable genomes-to-report pipeline. It contains all the essential tools to thoroughly characterize microbial genomes.
📇 CompareM2 even auto-generates a full-bodied report with interpretable information and publication ready graphics from the analyses of your own genomes.
🦠 Being designed to analyze assemblies of both isolates and metagenomes (MAGs), it is useful for anyone working with microbial genomics.
💾 Installing CompareM2 on your system gives you access to many powerful state-of-the-art tools for analysis of prokaryotic genomes which will accelerate your research. It is easy to use and can be used by non-bioinformaticians.
👩🔬 CompareM2 integrates several analyses that yield scientific results about genomic assemblies on several levels: Quality control, phylogenetics, pan/core genome, anti-microbial resistance and virulence profiling, species detection, pathway annotation, metabolic modeling and much more. And new tools are continuously added.
🐍 CompareM2 works by calling a Snakemake workflow that can be easily modified to use different parameters for the underlying tools.
📄 Central results are dynamically integrated in a compact portable report .html-document. It can be browsed in any web browser and can be easily shared as a single file. This report is generated even if some jobs in the pipeline fail. See examples.
🧑💻 CompareM2 can be run either on a local workstation (recommended >= 64GiB RAM), or a HPC (high performance computing) cluster. Both Apptainer/Singularity/Docker images and conda environment definitions are available for all dependent software to run.
🙋 If you have any questions, issues or ideas about using CompareM2, please raise an issue here.
📙 The comprehensive documentation is available at CompareM2.readthedocs.io, and the code base is available at github.com/cmkobel/CompareM2.