{"id":32588046,"url":"https://github.com/pdimens/djinn","last_synced_at":"2026-03-05T18:04:30.432Z","repository":{"id":313942066,"uuid":"1053513684","full_name":"pdimens/djinn","owner":"pdimens","description":"Convert linked-read FASTQ/BAM files between formats, almost like magic.","archived":false,"fork":false,"pushed_at":"2026-02-16T14:46:45.000Z","size":3146,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":0,"default_branch":"main","last_synced_at":"2026-02-16T22:28:51.541Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://pdimens.github.io/djinn/","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":null,"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,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2025-09-09T14:51:42.000Z","updated_at":"2026-02-16T14:44:59.000Z","dependencies_parsed_at":"2025-09-09T18:51:54.555Z","dependency_job_id":"f0b2b2ed-d828-40a9-be36-e07eb639bd33","html_url":"https://github.com/pdimens/djinn","commit_stats":null,"previous_names":["pdimens/djinn"],"tags_count":5,"template":false,"template_full_name":null,"purl":"pkg:github/pdimens/djinn","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pdimens%2Fdjinn","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pdimens%2Fdjinn/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pdimens%2Fdjinn/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pdimens%2Fdjinn/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/pdimens","download_url":"https://codeload.github.com/pdimens/djinn/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pdimens%2Fdjinn/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":30141324,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-03-05T16:58:46.102Z","status":"ssl_error","status_checked_at":"2026-03-05T16:58:45.706Z","response_time":93,"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":[],"created_at":"2025-10-29T23:54:05.861Z","updated_at":"2026-03-05T18:04:30.411Z","avatar_url":"https://github.com/pdimens.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"![djinn logo](https://raw.githubusercontent.com/pdimens/djinn/refs/heads/docs/static/djinn.png)\n\n[![GitHub Release](https://img.shields.io/github/v/release/pdimens/djinn?style=for-the-badge\u0026logo=anaconda\u0026logoColor=ffffff)](https://github.com/pdimens/djinn/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/djinn)\n[![GitHub Actions Workflow Status](https://img.shields.io/github/actions/workflow/status/pdimens/djinn/tests.yaml?style=for-the-badge\u0026logo=cachet\u0026logoColor=ffffff)](https://www.youtube.com/watch?v=F1qdBPlK9M4)\n\nModify and convert linked-read FASTQ and BAM files\n\n## Extract barcodes\nGet all the barcodes from the input file(s)\n\n## Sort by barcode\nSort records by barcode rather than name or position\n\n## Filtering\n- separate linked reads from singletons\n- omit invalid barcodes\n\n## Convert files\nDjinn converts between linked-read data formats. You can convert between formats in terms of FASTQ type or barcode style. It supports:\n- 10X\n- haplotagging\n- stLFR\n- TELLseq\n- [standard](https://pdimens.github.io/harpy/getting_started/linked_read_data/#linked-read-data-types)\n\n## NCBI submission\nNCBI strips out sequence headers from FASTQ submissions, so it would be best to convert your linked-read\nFASTQ data into an unaligned BAM file, with the linked-read barcode stored in the `BX` or `BC` tag.\nDjinn provides a convenience function to convert to (or from) this format, although it's really just\na basic `samtools` command.\n\n## Hi-C spoofing\nThis is **extremely experimental** and it converts a paired-end linked-read fastq file pair into one that conforms to Hi-C expectations by mix-matching the R1s and R2s of reads that share a barcode.","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpdimens%2Fdjinn","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpdimens%2Fdjinn","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpdimens%2Fdjinn/lists"}