{"id":37674156,"url":"https://github.com/signaturescience/metscale","last_synced_at":"2026-01-16T12:09:53.668Z","repository":{"id":40955561,"uuid":"147439899","full_name":"signaturescience/metscale","owner":"signaturescience","description":"MetScale: snakemake workflows to scale metagenome analyses","archived":false,"fork":false,"pushed_at":"2025-05-15T15:52:19.000Z","size":388225,"stargazers_count":19,"open_issues_count":9,"forks_count":10,"subscribers_count":12,"default_branch":"master","last_synced_at":"2025-05-15T16:48:28.754Z","etag":null,"topics":["metagenomics","open-source","snakemake-workflows","taxonomic-classifications"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/signaturescience.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2018-09-05T01:08:17.000Z","updated_at":"2025-05-15T15:52:24.000Z","dependencies_parsed_at":"2023-01-19T23:35:04.152Z","dependency_job_id":"9c35a780-4f57-43d7-a8c9-39c32d8c32fd","html_url":"https://github.com/signaturescience/metscale","commit_stats":null,"previous_names":[],"tags_count":5,"template":false,"template_full_name":null,"purl":"pkg:github/signaturescience/metscale","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/signaturescience%2Fmetscale","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/signaturescience%2Fmetscale/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/signaturescience%2Fmetscale/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/signaturescience%2Fmetscale/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/signaturescience","download_url":"https://codeload.github.com/signaturescience/metscale/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/signaturescience%2Fmetscale/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28478479,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-16T11:59:17.896Z","status":"ssl_error","status_checked_at":"2026-01-16T11:55:55.838Z","response_time":107,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["metagenomics","open-source","snakemake-workflows","taxonomic-classifications"],"created_at":"2026-01-16T12:09:52.881Z","updated_at":"2026-01-16T12:09:53.659Z","avatar_url":"https://github.com/signaturescience.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# MetScale IS NOT CURRENTLY UNDER ACTIVE DEVELOPMENT\n\nWe are always interested in additional teaming opportunities, or new feature requests, however at this time, we are not actively developing MetScale.  \n\nIf you have inquires about metscale, please submit issues, or contact SigSci directly.\n\n\n\n\n\n![](https://github.com/signaturescience/metagenomics/blob/master/documentation/figures/MetScale_Logo.png)\n\n\n\n# MetScale: open source metagenomics workflows\n\nThese 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. \n\n![](https://github.com/signaturescience/metagenomics/blob/master/documentation/figures/Overview_Flowchart.png)\n\n## Getting Started\n\nThe [wiki](https://github.com/signaturescience/metagenomics/wiki) for this project has helpful instructions for installing and running the workflows.\n\n## Prerequisites\n\nThese workflows have been tested to run offline on Linux operating systems, including CentOS, Red Hat, and Ubuntu.\n\n## Example Data \n\nThe workflows have been tested with a subsampled dataset from this publication:\n\n[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/)\n \nThe 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:\n\n[SRR606249_subset10_1.fq.gz](https://osf.io/xwk7m/)\n\n[SRR606249_subset10_2.fq.gz](https://osf.io/6dmh5/)\n\n## Contributing\n\nPlease 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.\n\n## License\n\nThis software is licensed under the [BSD 3-Clause License](https://github.com/signaturescience/metagenomics/blob/master/LICENSE).\n\n## Acknowledgments\n\nThis 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. \n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsignaturescience%2Fmetscale","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsignaturescience%2Fmetscale","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsignaturescience%2Fmetscale/lists"}