{"id":21873638,"url":"https://github.com/snitkin-lab-umich/data-flow-sop","last_synced_at":"2025-08-11T06:19:59.818Z","repository":{"id":253120548,"uuid":"841519118","full_name":"Snitkin-Lab-Umich/Data-Flow-SOP","owner":"Snitkin-Lab-Umich","description":"SOPs for processing short, long, and hybrid bacterial data","archived":false,"fork":false,"pushed_at":"2025-01-21T16:14:39.000Z","size":789,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-01-21T17:25:51.563Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://github.com/Snitkin-Lab-Umich/Data-Flow-SOP/wiki","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Snitkin-Lab-Umich.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"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}},"created_at":"2024-08-12T15:09:42.000Z","updated_at":"2025-01-21T16:31:10.000Z","dependencies_parsed_at":"2024-11-08T16:27:42.567Z","dependency_job_id":"3e0bb9a6-07d2-41bf-9571-1b1b780d7df8","html_url":"https://github.com/Snitkin-Lab-Umich/Data-Flow-SOP","commit_stats":null,"previous_names":["snitkin-lab-umich/data-flow-sop"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Snitkin-Lab-Umich%2FData-Flow-SOP","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Snitkin-Lab-Umich%2FData-Flow-SOP/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Snitkin-Lab-Umich%2FData-Flow-SOP/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Snitkin-Lab-Umich%2FData-Flow-SOP/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Snitkin-Lab-Umich","download_url":"https://codeload.github.com/Snitkin-Lab-Umich/Data-Flow-SOP/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":244880660,"owners_count":20525515,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","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":[],"created_at":"2024-11-28T07:08:57.884Z","updated_at":"2025-03-21T23:16:20.275Z","avatar_url":"https://github.com/Snitkin-Lab-Umich.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Data Flow SOP\n\nThis repository outlines the steps for processing data as part of the [Snitkin Lab](https://thesnitkinlab.com/index.php) Data Flow Standard Operating Procedure (SOP). The Data Flow SOP details how to process your samples after they've been sequenced by either the Genomics Core or Plasmidsaurus. To begin, select the guide that corresponds to your sample type—Illumina, Nanopore, or hybrid (Illumina + Nanopore).\n\n## Available Workflows\n\n### 1. **Illumina Samples**\nThe necessary files for Nanopore workflow can be found in the `illumina/` directory. For detailed instructions on processing Illumina sequencing data, refer to the following documentation:\n- [Processing Illumina Samples](processing-illumina-samples.md)\n\nYou can also explore the related scripts and files in the current directory:\n- `create_directories.py`\n- `create_higher_level_dirs.py`\n\n### 2. **Nanopore Samples**\nThe necessary files for Nanopore workflow can be found in the `nanopore/` directory. If you're working with Nanopore sequencing data, please consult the guide below:\n- [Processing Nanopore Samples](processing-nanopore-samples.md)\n\n### 3. **Hybrid Samples (Illumina + Nanopore)**\n*This section is coming soon.*\n\n\u003c!-- For hybrid samples that involve both Illumina and Nanopore data, use the following instructions:\n- [Processing Hybrid Samples](processing-hybrid-samples.md)\n\u003c!-- \nCheck the `hybrid/` directory for additional tools specific to hybrid workflows.\n--\u003e\n## Directory Structure\n\nThis repository is organized as follows:\n\n```\nData-Flow-SOP\n├── create_directories.py\n├── create_higher_level_dirs.py\n├── illumina\n│   ├── move_files_to_directories_illumina.py\n│   └── rename_samples_illumina.sh\n├── nanopore\n│   ├── move_files_to_dirs_nanopore.py\n│   └── rename_samples_nanopore.sh\n├── pics\n│   ├── globus-raw-fastq-nanopore.png\n│   ├── globus_raw_fastq.png\n│   ├── transfer-nanoQC-results.png\n│   └── transfer-qcd-results.png\n├── processing-hybrid-samples.md\n├── processing-illumina-samples.md\n├── processing-nanopore-samples.md\n└── README.md\n\n```\n\nTo begin, select the appropriate workflow based on your sequencing method and follow the corresponding guide.\n\nFor any questions or issues, please open an issue on [Github](https://github.com/Snitkin-Lab-Umich/Data-Flow-SOP/issues). For urgent inquiries, contact Dhatri on Slack or via email at dhatrib@umich.edu.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsnitkin-lab-umich%2Fdata-flow-sop","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsnitkin-lab-umich%2Fdata-flow-sop","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsnitkin-lab-umich%2Fdata-flow-sop/lists"}