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CompareM2

GitHub last commit GitHub Actions Workflow Status Bioconda downloads Docker Pulls Documentation Status Conda Version https://doi.org/10.1101/2024.07.12.603264 GitHub Repo stars

!!! 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 genomes-to-report pipeline. It accepts prokaryotic (bacterial and archaeal) genomic assemblies and compares them in many different ways.

🦠 Being designed to analyze assemblies of both isolates and metagenomes (MAGs), it is useful for anyone working with microbial genomics.

πŸ’Ύ 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.

πŸ‘©β€πŸ”¬ CompareM2 integrates several analyses that yield scientific results about genomic assemblies on several levels: Quality control, annotation, function and species calling as well as comparative analyses like computation of core/pan genomes and phylogenetics.

🐍 CompareM2 works by calling a Snakemake workflow that can be easily modified to use different parameters for the underlying tools.

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πŸ“„ 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.

πŸ§‘β€πŸ’» 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.

πŸ™‹ If you have any questions, issues or ideas about using CompareM2, please raise an issue here.

πŸ“™ The comprehensive documentation is available at CompareM2.readthedocs.io. And the code base is available at github.com/cmkobel/CompareM2.


CompareM2 genomes-to-report pipeline. Copyright (C) 2024 contributors GNU GPL v3.