{"id":46940983,"url":"https://github.com/datacarpentry/wrangling-genomics","last_synced_at":"2026-03-11T07:03:49.919Z","repository":{"id":29282493,"uuid":"32815233","full_name":"datacarpentry/wrangling-genomics","owner":"datacarpentry","description":"Data Wrangling and Processing for Genomics","archived":false,"fork":false,"pushed_at":"2026-03-10T00:37:38.000Z","size":76921,"stargazers_count":73,"open_issues_count":51,"forks_count":151,"subscribers_count":22,"default_branch":"main","last_synced_at":"2026-03-10T08:10:17.331Z","etag":null,"topics":["carpentries","data-carpentry","data-wrangling","english","genomics","lesson","programming","shell","stable"],"latest_commit_sha":null,"homepage":"https://datacarpentry.org/wrangling-genomics/","language":"Shell","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/datacarpentry.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE.md","code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":"CITATION","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":"AUTHORS","dei":null,"publiccode":null,"codemeta":null,"zenodo":".zenodo.json","notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null},"funding":{"github":["carpentries"],"custom":["https://www.zeffy.com/en-US/donation-form/donate-to-make-a-difference-7497"]}},"created_at":"2015-03-24T17:51:36.000Z","updated_at":"2026-02-14T20:35:43.000Z","dependencies_parsed_at":"2023-12-26T01:27:51.620Z","dependency_job_id":"8ccd7f14-ce27-44a2-9648-dd9f58585e71","html_url":"https://github.com/datacarpentry/wrangling-genomics","commit_stats":null,"previous_names":[],"tags_count":3,"template":false,"template_full_name":null,"purl":"pkg:github/datacarpentry/wrangling-genomics","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/datacarpentry%2Fwrangling-genomics","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/datacarpentry%2Fwrangling-genomics/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/datacarpentry%2Fwrangling-genomics/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/datacarpentry%2Fwrangling-genomics/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/datacarpentry","download_url":"https://codeload.github.com/datacarpentry/wrangling-genomics/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/datacarpentry%2Fwrangling-genomics/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":30373523,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-03-11T06:09:32.197Z","status":"ssl_error","status_checked_at":"2026-03-11T06:09:17.086Z","response_time":84,"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":["carpentries","data-carpentry","data-wrangling","english","genomics","lesson","programming","shell","stable"],"created_at":"2026-03-11T07:03:46.202Z","updated_at":"2026-03-11T07:03:49.895Z","avatar_url":"https://github.com/datacarpentry.png","language":"Shell","readme":"[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3260609.svg)](https://doi.org/10.5281/zenodo.3260609)\n[![Create a Slack Account with us](https://img.shields.io/badge/Create_Slack_Account-The_Carpentries-071159.svg)](https://slack-invite.carpentries.org/)\n[![Slack Status](https://img.shields.io/badge/Slack_Channel-dc--genomics-E01563.svg)](https://carpentries.slack.com/messages/C9N1K7DCY)\n\n# Wrangling Genomics\n\nLesson for quality control and wrangling genomics data. This repository is maintained by [Josh Herr](https://github.com/jrherr), [Ming Tang](https://github.com/crazyhottommy), and [Fotis Psomopoulos](https://github.com/fpsom).\n\nAmazon public AMI for this tutorial is \"dataCgen-qc\".\n\n## Background\n\nWrangling genomics trains novice learners on a variant calling workflow. Participants will learn how to evaluate sequence quality and what to do if it is not good. We will then cover aligning reads to a genome, and calling variants, as well as discussing different file formats. Results will be visualized. Finally, we will cover how to automate the process by building a shell script.\n\nThis lesson is part of the [Data Carpentry](https://www.datacarpentry.org/) [Genomics Workshop](https://www.datacarpentry.org/genomics-workshop/).\n\n## Contribution\n\n- Make a suggestion or correct an error by [raising an Issue](https://github.com/datacarpentry/wrangling-genomics/issues).\n\n## Code of Conduct\n\nAll participants should agree to abide by the [Data Carpentry Code of Conduct](https://www.datacarpentry.org/code-of-conduct/).\n\n## Authors\n\nWrangling genomics is authored and maintained by the [community](https://github.com/datacarpentry/wrangling-genomics/network/members).\n\n## Citation\n\nPlease cite as:\n\nErin Alison Becker, Taylor Reiter, Fotis Psomopoulos, Sheldon John McKay, Jessica Elizabeth Mizzi, Jason Williams, … Winni Kretzschmar. (2019, June). datacarpentry/wrangling-genomics: Data Carpentry: Genomics data wrangling and processing, June 2019 (Version v2019.06.1). Zenodo. [http://doi.org/10.5281/zenodo.3260609](https://doi.org/10.5281/zenodo.3260609)\n\n\n","funding_links":["https://github.com/sponsors/carpentries","https://www.zeffy.com/en-US/donation-form/donate-to-make-a-difference-7497"],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdatacarpentry%2Fwrangling-genomics","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdatacarpentry%2Fwrangling-genomics","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdatacarpentry%2Fwrangling-genomics/lists"}