Science Score: 57.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
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✓codemeta.json file
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✓.zenodo.json file
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✓DOI references
Found 4 DOI reference(s) in README -
○Academic publication links
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○Scientific vocabulary similarity
Low similarity (14.5%) to scientific vocabulary
Keywords
Repository
🦠🧬🧑💻📇 Microbial genomes-to-report pipeline
Basic Info
- Host: GitHub
- Owner: cmkobel
- License: gpl-3.0
- Language: Python
- Default Branch: master
- Homepage: https://CompareM2.readthedocs.io
- Size: 110 MB
Statistics
- Stars: 59
- Watchers: 2
- Forks: 3
- Open Issues: 20
- Releases: 32
Topics
Metadata Files
README.md
CompareM2
!!! 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.
Owner
- Name: Carl Mathias Kobel
- Login: cmkobel
- Kind: user
- Company: Norges Miljø- & Biovitenskapelige Universitet
- Website: https://orcid.org/0000-0002-4461-1159
- Repositories: 49
- Profile: https://github.com/cmkobel
PhD-fellow in the MEMO group at NMBU.
Citation (citation.cff)
cff-version: 1.2.0 message: "If you like Comparem2, you can support further funding by citing it." authors: - family-names: "Kobel" given-names: "Carl M." orcid: "https://orcid.org/0000-0002-4461-1159" - family-names: "Aho" given-names: "Velma T. E." orcid: "http://orcid.org/0000-0003-2916-7018" - family-names: "Øyås" given-names: "Ove" orcid: "http://orcid.org/0000-0001-6990-0339" - family-names: "Nørskov-Lauritsen" given-names: "Niels" orcid: "http://orcid.org/0000-0001-5520-106X" - family-names: "Woodcroft" given-names: "Ben J." orcid: "http://orcid.org/0000-0003-0670-7480" - family-names: "Pope" given-names: "Phillip B." orcid: "http://orcid.org/0000-0002-2067-4059" title: "CompareM2 is a genomes-to-report pipeline for comparing microbial genomes" version: 2 doi: 10.1101/2024.07.12.603264 date-released: 2024-07-17 url: "https://github.com/cmkobel/CompareM2"
GitHub Events
Total
- Create event: 4
- Commit comment event: 2
- Release event: 5
- Issues event: 20
- Watch event: 4
- Issue comment event: 24
- Push event: 213
Last Year
- Create event: 4
- Commit comment event: 2
- Release event: 5
- Issues event: 20
- Watch event: 4
- Issue comment event: 24
- Push event: 213
Dependencies
- condaforge/mambaforge latest build
- markdown-include *
- mkdocs *
- mkdocstrings *
- click ==8.1.3
- ghp-import ==2.1.0
- griffe ==0.22.0
- importlib-metadata ==4.12.0
- jinja2 ==3.1.2
- markdown ==3.3.7
- markdown-include ==0.6.0
- markupsafe ==2.1.1
- mergedeep ==1.3.4
- mkdocs ==1.3.0
- mkdocs-autorefs ==0.4.1
- mkdocstrings ==0.19.0
- mkdocstrings-python ==0.7.1
- packaging ==21.3
- pymdown-extensions ==9.5
- pyparsing ==3.0.9
- python-dateutil ==2.8.2
- pyyaml ==6.0
- pyyaml-env-tag ==0.1
- six ==1.16.0
- watchdog ==2.1.9
- zipp ==3.8.0
- actions/checkout v4 composite
- conda-incubator/setup-miniconda v3 composite
- actions/checkout v2 composite
- conda-incubator/setup-miniconda v2 composite
- actions/checkout v2 composite
- conda-incubator/setup-miniconda v2 composite
- actions/checkout v2 composite
- conda-incubator/setup-miniconda v2 composite
- actions/checkout v2 composite
- conda-incubator/setup-miniconda v2 composite
- mamba <2
- pandas
- pulp <2.8
- python <3.12
- snakemake-minimal <8