{"id":13408073,"url":"https://github.com/pdimens/harpy","last_synced_at":"2026-02-03T22:00:44.100Z","repository":{"id":63684244,"uuid":"567840239","full_name":"pdimens/harpy","owner":"pdimens","description":"Process linked-read data, from raw sequences to phased haplotypes, batteries included. Works with WGS too!","archived":false,"fork":false,"pushed_at":"2026-02-02T21:22:35.000Z","size":499048,"stargazers_count":18,"open_issues_count":7,"forks_count":2,"subscribers_count":1,"default_branch":"main","last_synced_at":"2026-02-03T10:57:43.987Z","etag":null,"topics":["bioinformatics","haplotype","linked-reads","pipeline","sequencing","variant-calling"],"latest_commit_sha":null,"homepage":"https://pdimens.github.io/harpy","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/pdimens.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":".github/CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":".github/CODE_OF_CONDUCT.md","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,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2022-11-18T17:51:21.000Z","updated_at":"2026-02-02T20:08:27.000Z","dependencies_parsed_at":"2024-05-29T23:43:55.769Z","dependency_job_id":"3b320902-07f9-4f8d-92a1-a9f610dad9d4","html_url":"https://github.com/pdimens/harpy","commit_stats":{"total_commits":2091,"total_committers":1,"mean_commits":2091.0,"dds":0.0,"last_synced_commit":"ee8a29fdc2dec4259ba6a08463c658afaa470651"},"previous_names":[],"tags_count":65,"template":false,"template_full_name":null,"purl":"pkg:github/pdimens/harpy","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pdimens%2Fharpy","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pdimens%2Fharpy/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pdimens%2Fharpy/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pdimens%2Fharpy/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/pdimens","download_url":"https://codeload.github.com/pdimens/harpy/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pdimens%2Fharpy/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29058972,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-03T20:13:53.544Z","status":"ssl_error","status_checked_at":"2026-02-03T20:13:40.507Z","response_time":96,"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":["bioinformatics","haplotype","linked-reads","pipeline","sequencing","variant-calling"],"created_at":"2024-07-30T20:00:50.593Z","updated_at":"2026-02-03T22:00:44.091Z","avatar_url":"https://github.com/pdimens.png","language":"Python","readme":"[![logo](https://github.com/pdimens/harpy/blob/docs/static/logo_trans.png?raw=true)](https://pdimens.github.io/harpy)\n\n[![GitHub Release](https://img.shields.io/github/v/release/pdimens/harpy?style=for-the-badge\u0026logo=anaconda\u0026logoColor=ffffff)](https://github.com/pdimens/harpy/releases)\n[![documentation badge](https://img.shields.io/badge/read%20the-docs-fbab3a?style=for-the-badge\u0026logo=quicklook\u0026logoColor=ffffff)](https://pdimens.github.io/harpy)\n[![GitHub Actions Workflow Status](https://img.shields.io/github/actions/workflow/status/pdimens/harpy/tests.yml?style=for-the-badge\u0026logo=cachet\u0026logoColor=ffffff)](https://www.youtube.com/watch?v=F1qdBPlK9M4)\n[![haplotagging badge](https://custom-icon-badges.demolab.com/badge/-Haplotagging-8879b9?style=for-the-badge\u0026logo=grapheneos\u0026logoColor=ffffff)](https://www.fml.tuebingen.mpg.de/9418/haplotagging)\n\n[Linked-read](https://doi.org/10.1073/pnas.2015005118) data processing pipeline. Getting you from raw linked reads to assemblies, genotypes, or phased haplotypes. Batteries included 🔋\n\n\u003cp align=\"center\"\u003e\n✨ Now works with TELLseq, stLFR, and non-linked read data! ✨\n\u003c/p\u003e\n\n## 📥 Install\nDetailed installation instructions are described in [the documentation](https://pdimens.github.io/harpy/install/). \n### 🐍 Conda\n```bash\nconda create -n harpy -c bioconda -c conda-forge harpy\nconda activate harpy\n```\n\n### 🌟 Pixi\n```bash\npixi global install -c conda-forge -c bioconda harpy\n# or locally #\npixi init -c conda-forge -c bioconda projectname \u0026\u0026 cd projectname \u0026\u0026 pixi add harpy\n```\n\n### 📦 Containers\n#### 🐳 Docker\n```bash\ndocker pull quay.io/biocontainers/harpy\n```\n\n#### 🅰️ Apptainer\nFind the most recent tag [here](https://quay.io/repository/biocontainers/harpy?tab=tags) and replace `$TAG` with it or use the `TAG=$(curl ...)` part below to pull the latest version name using the repository's API.\n```bash\nTAG=$(curl -s \"https://quay.io/api/v1/repository/biocontainers/harpy/tag/\" | cut -d'\"' -f6)\napptainer pull docker://quay.io/biocontainers/harpy:$TAG\n```\n\n## ⚡ Usage\nJust call `harpy` or `harpy --help` on the command line to get started! If installed via container, then call the containerized-Harpy however you are used to using containers on your system.\n\n```bash\nharpy module options... args...\n```\n\n## 🌈 Getting Started\nNo data? No problem! Use [HACk](https://davidebolo1993.github.io/visordoc/usecases/usecases.html#visor-hack) to simulate genomic variants from an existing genome and use [Mimick](https://pdimens.github.io/mimick/#/) to create linked-read data from an existing genome! You can see what haplotagging (or other linked read) data and Harpy are like without investing a single cent! A real-world walkthrough of how we did this for a benchmarking experiment can be found [here](https://pdimens.github.io/LRInversionSimulations/).\n\n## Citation\n\u003eDimens PV, Franckowiak RP, Iqbal A, Grenier JK, Munn PR, Therkildsen NO. Harpy: a pipeline for processing haplotagging linked-read data. Bioinform Adv. 2025 Jun 5;5(1):vbaf133. doi: [10.1093/bioadv/vbaf133](https://pubmed.ncbi.nlm.nih.gov/40575478/). PMID: 40575478; PMCID: PMC12198493.","funding_links":[],"categories":["Tools"],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpdimens%2Fharpy","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpdimens%2Fharpy","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpdimens%2Fharpy/lists"}