https://github.com/signaturescience/metscale
MetScale: snakemake workflows to scale metagenome analyses
https://github.com/signaturescience/metscale
metagenomics open-source snakemake-workflows taxonomic-classifications
Last synced: 5 months ago
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MetScale: snakemake workflows to scale metagenome analyses
- Host: GitHub
- URL: https://github.com/signaturescience/metscale
- Owner: signaturescience
- License: bsd-3-clause
- Created: 2018-09-05T01:08:17.000Z (almost 8 years ago)
- Default Branch: master
- Last Pushed: 2025-05-15T15:52:19.000Z (about 1 year ago)
- Last Synced: 2025-05-15T16:48:28.754Z (about 1 year ago)
- Topics: metagenomics, open-source, snakemake-workflows, taxonomic-classifications
- Language: Python
- Homepage:
- Size: 370 MB
- Stars: 19
- Watchers: 12
- Forks: 10
- Open Issues: 9
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Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
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README
# MetScale IS NOT CURRENTLY UNDER ACTIVE DEVELOPMENT
We are always interested in additional teaming opportunities, or new feature requests, however at this time, we are not actively developing MetScale.
If you have inquires about metscale, please submit issues, or contact SigSci directly.
# MetScale: open source metagenomics workflows
These open source metagenomics workflows are intended to analyze the biological contents of complex environmental samples. The expected input is paired-end Illumina FASTQ files, and the current outputs include filtered reads, assembled contigs, MultiQC reports for FastQC and QUAST results, metagenome comparison estimates, taxonomic classifications, and functional predictions.
## Getting Started
The [wiki](https://github.com/signaturescience/metagenomics/wiki) for this project has helpful instructions for installing and running the workflows.
## Prerequisites
These workflows have been tested to run offline on Linux operating systems, including CentOS, Red Hat, and Ubuntu.
## Example Data
The workflows have been tested with a subsampled dataset from this publication:
[Shakya, M., C. Quince, J. H. Campbell, Z. K. Yang, C. W. Schadt and M. Podar (2013). "Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities." Environ Microbiol 15(6): 1882-1899.](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3665634/)
The original Shakya et al. 2013 dataset is available online as [SRR606249](https://www.ebi.ac.uk/ena/data/view/SRR606249). The subsampled dataset, which was used as the default example in our metagenomics workflows, can be downloaded here:
[SRR606249_subset10_1.fq.gz](https://osf.io/xwk7m/)
[SRR606249_subset10_2.fq.gz](https://osf.io/6dmh5/)
## Contributing
Please read [CONTRIBUTING.md](https://github.com/signaturescience/metagenomics/blob/master/CONTRIBUTING.md) for details on our code of conduct and how to contribute to this project.
## License
This software is licensed under the [BSD 3-Clause License](https://github.com/signaturescience/metagenomics/blob/master/LICENSE).
## Acknowledgments
This project builds off work that began in the [Dahak project](https://github.com/dahak-metagenomics/dahak). A variety of open source tools are used within the workflows, and more information about those tools is available in the [DEPENDENCY_LICENSES](https://github.com/signaturescience/metagenomics/blob/master/DEPENDENCY_LICENSES) file.