Mixed Microbial Analysis on sequencing data - MMAseq

MMAseq is a modular Snakemake-driven workflow that utilizes public tools and custom scripts to coordinate and execute analysis if whole genome microbial sequencing data. It is designed with a configuration based architecture in mind, to facilitate control over the flow of analysis. The modular structure and configuration based architecture enables the user to execute species-specific analysis of a wealth of different species from a single execution.

The pipeline utilizes raw reads and assemblies. In case assemblies are missing, the pipeline offers a few options for de-novo assemblies.

Tools

MMAseq currently includes 30+ different bioinformatic tools, which will expand in the future. The included tools enables the pipeline to support Assembly, characterization through CGE finders, characterization through NCBI tools, Configurable custom SNP and deletion identification

Documentation

A complete documentation is available MMAseq Documentation. The documentation includes a full guide to the workflow from installation, tutorials, bacterial species supported etc...

Contributing

Please to report bugs or enhancement use the Issue Tracker.

Citation

When using SSI analysis in published work, please cite the following:

[PLACEHOLDER FOR CITATION INSTRUCTION]

For citations of included algorithms and sub-modules please see the references

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Publisher: publish.yml on ssi-dk/MMASeq

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- Predicate type: https://docs.pypi.org/attestations/publish/v1
- Subject name: mmaseq-2.0.0.tar.gz
- Subject digest: a68740fc360e1a09e3d604be6780730b81798e5e5fcdc760e03d639f15909856
- Sigstore transparency entry: 2466099397
- Sigstore integration time: Aug 14, 2026
Source repository:
- Permalink: ssi-dk/MMASeq@073957bc807bc2d3957e8f58a4d93abe024983da
- Branch / Tag: refs/tags/v2.0.0
- Owner: https://github.com/ssi-dk
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- Trigger Event: release