{"id":28328207,"url":"https://github.com/niaid/microbiome","last_synced_at":"2026-01-31T18:31:45.639Z","repository":{"id":89672809,"uuid":"206605984","full_name":"niaid/microbiome","owner":"niaid","description":"Microbiome Data Analysis and Nephele Demo","archived":false,"fork":false,"pushed_at":"2019-09-12T05:36:52.000Z","size":15,"stargazers_count":1,"open_issues_count":0,"forks_count":1,"subscribers_count":5,"default_branch":"master","last_synced_at":"2025-08-12T00:47:28.024Z","etag":null,"topics":["bcbb-training","microbiome","microbiome-analysis"],"latest_commit_sha":null,"homepage":"","language":null,"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/niaid.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}},"created_at":"2019-09-05T16:10:17.000Z","updated_at":"2022-08-16T19:48:08.000Z","dependencies_parsed_at":null,"dependency_job_id":"1852421a-3657-4c2f-af86-f2560e67c4b8","html_url":"https://github.com/niaid/microbiome","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/niaid/microbiome","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/niaid%2Fmicrobiome","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/niaid%2Fmicrobiome/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/niaid%2Fmicrobiome/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/niaid%2Fmicrobiome/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/niaid","download_url":"https://codeload.github.com/niaid/microbiome/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/niaid%2Fmicrobiome/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28949370,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-31T18:30:42.805Z","status":"ssl_error","status_checked_at":"2026-01-31T18:30:19.593Z","response_time":128,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: 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":["bcbb-training","microbiome","microbiome-analysis"],"created_at":"2025-05-26T06:16:14.754Z","updated_at":"2026-01-31T18:31:45.634Z","avatar_url":"https://github.com/niaid.png","language":null,"funding_links":[],"categories":[],"sub_categories":[],"readme":"# microbiome\nMicrobiome Data Analysis and Nephele Demo\n\n### Nephele Web Server\n\u003chttps://nephele.niaid.nih.gov\u003e\n\n### Resources for RML session on Microbiome Data Analysis ###\n1. Slides - [download pdf of slides here](https://proj-bip-prod-publicread.s3.amazonaws.com/training/Microbiome+and+Nephele/Microbiome_RML.pdf)\n\n2. Test input files: for 16S pipelines\n    Download sequences and mapping files from \"How to submit a job\" - \u003chttps://nephele.niaid.nih.gov/user_guide/\u003e\n\n#### Steps to run Demo.  For more details see: https://nephele.niaid.nih.gov/user_guide/\n1. Request account in nephele server\n2. Select Amplicon Data, 16S\n3. Sign into Nephele with the email you registered with, then select **Paired End Fastq**\n4. Select **\"Upload files from publicly accessible URL(s)\", Upload via FTP** . Provide the following path **ftp://helix.nih.gov/pub/mqbcbb/nepheleFQ/**  Please know that this folder will be available only temporarily from this FTP location.  \n5. Download file from **\u003cftp://helix.nih.gov/pub/mqbcbb/N2_16S_mapping.xlsx\u003e** then upload to Nephele as the mapping file. \n6. Follow along to submit a job.  THere is no need to change default parameters for this dataset.   \n7. Expect an email with words \"nephele pipeline success\"\n\n#### View results\n\n1. [Download DADA2 example output here](https://nephele-prod-testdata.s3.amazonaws.com/dada_example_output.zip)\n\n2. Alternatively, if you run the job, expect an email with note that job has completed \u003chttps://nephele.niaid.nih.gov/results/f04730b61840\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fniaid%2Fmicrobiome","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fniaid%2Fmicrobiome","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fniaid%2Fmicrobiome/lists"}