Metadata-Version: 2.4
Name: MMAseq
Version: 1.0
Summary: Mixed Microbial Analysis on Sequencing data
Project-URL: Documentation, https://ssi-dk.github.io/MMASeq
Project-URL: Repository, https://github.com/ssi-dk/MMASeq
Author-email: Kasper Thystrup Karstensen <kathka@gmail.com>, Simone Scrima <simonescrima@gmail.com>
Maintainer-email: Kasper Thystrup Karstensen <kathka@gmail.com>, Simone Scrima <simonescrima@gmail.com>
License: The MIT License (MIT)
        Copyright © 2023 Statens Serum Institut
        
        Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
        
        THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
License-File: LICENSE
Requires-Python: >=3.13
Requires-Dist: pandas
Requires-Dist: snakemake
Description-Content-Type: text/markdown

# Mixed Microbial Analysis on sequencing data - MMAseq
[![Snakemake](https://img.shields.io/badge/snakemake-v7.32-blue?logo=snakemake)](https://snakemake.readthedocs.io/)
[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](./LICENSE)

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](https://ssi-dk.github.io/MMASeq/). 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](https://ssi-dk.github.io/MMASeq/references/)
