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
1 maintainer
Release files for mmaseq 2.3.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| mmaseq-2.3.0.tar.gz | 17.3 MB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| mmaseq-2.3.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 34.9 MB
Release files / mmaseq-2.3.0.tar.gz
| Download URL | mmaseq-2.3.0.tar.gz |
|---|---|
| Size | 17.3 MB |
| Tags | Source |
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SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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twine/7.0.0 CPython/3.13.14
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Transparency logRelease files / mmaseq-2.3.0-py3-none-any.whl
| Download URL | mmaseq-2.3.0-py3-none-any.whl |
|---|---|
| Size | 17.6 MB |
| Tags | Python 3 |
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SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
5efb5f4e18a80a84d686a29030bd806363fe8aad4fa533fe1fb95bd00fbeebc6
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| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Sep 25, 2026.
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