{"id":38990213,"url":"https://github.com/gear-genomics/halo","last_synced_at":"2026-01-17T17:02:13.045Z","repository":{"id":44117621,"uuid":"142536801","full_name":"gear-genomics/halo","owner":"gear-genomics","description":"Halo: Haplotype processor","archived":false,"fork":false,"pushed_at":"2025-12-27T18:56:52.000Z","size":6065,"stargazers_count":3,"open_issues_count":0,"forks_count":1,"subscribers_count":4,"default_branch":"main","last_synced_at":"2025-12-29T15:35:22.527Z","etag":null,"topics":["alignment","bam","haplotypes","single-cell"],"latest_commit_sha":null,"homepage":"https://www.gear-genomics.com/halo/","language":"C++","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/gear-genomics.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":"2018-07-27T06:26:17.000Z","updated_at":"2025-12-27T18:56:56.000Z","dependencies_parsed_at":"2025-06-24T08:22:21.454Z","dependency_job_id":"76451ff2-a5f4-4f86-9574-2fbd41b96842","html_url":"https://github.com/gear-genomics/halo","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/gear-genomics/halo","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gear-genomics%2Fhalo","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gear-genomics%2Fhalo/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gear-genomics%2Fhalo/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gear-genomics%2Fhalo/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/gear-genomics","download_url":"https://codeload.github.com/gear-genomics/halo/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gear-genomics%2Fhalo/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28511876,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-17T13:38:16.342Z","status":"ssl_error","status_checked_at":"2026-01-17T13:37:44.060Z","response_time":85,"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":["alignment","bam","haplotypes","single-cell"],"created_at":"2026-01-17T17:02:12.291Z","updated_at":"2026-01-17T17:02:13.036Z","avatar_url":"https://github.com/gear-genomics.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![C/C++ CI](https://github.com/gear-genomics/halo/workflows/C/C++%20CI/badge.svg)](https://github.com/gear-genomics/halo/actions)\n[![Docker CI](https://github.com/gear-genomics/halo/workflows/Docker%20CI/badge.svg)](https://hub.docker.com/r/geargenomics/halo/)\n[![GitHub Releases](https://img.shields.io/github/release/gear-genomics/halo.svg)](https://github.com/gear-genomics/halo/releases)\n\n# Halo: Haplotype processor\n\n[GEAR](https://www.gear-genomics.com/) hosts the `halo` web application at [https://www.gear-genomics.com/halo/](https://www.gear-genomics.com/halo/). The `halo` command-line tool is needed to compute the input file for the `halo` web application.\n\n## Installing halo\n\nThe `halo` command-line tool is available as a pre-compiled statically linked binary from [Halo's github release page](https://github.com/gear-genomics/halo/releases/), as a singularity container [SIF file](https://github.com/gear-genomics/halo/releases/) or as a minimal [Docker container](https://hub.docker.com/r/geargenomics/halo/).\n\n```bash\ngit clone --recursive https://github.com/gear-genomics/halo.git\ncd halo/\nmake all\nmake install\n```\n\n## Usage\n\nHalo is used to create the input JSON file for the [web application](https://www.gear-genomics.com/halo/).\n\n```bash\n./bin/halo -h\n```\n\nThis command-line application was designed for [Strand-Seq](https://en.wikipedia.org/wiki/Single-cell_DNA_template_strand_sequencing) single-cell DNA data but the viewer can also be used for any haplotype-resolved data. To convert the Strand-Seq alignment data into JSON format please provide one input BAM file for each input cell, e.g.:\n\n```bash\nhalo count -g hg38.fa -o sc.json.gz sc1.bam sc2.bam sc3.bam\n```\n\nThe output file `sc.json.gz` can then be uploaded and visualized at [https://www.gear-genomics.com/halo/](https://www.gear-genomics.com/halo/).\n\nLicense\n-------\nHalo is distributed under the GPLv3 license. Consult the accompanying [LICENSE](https://github.com/gear-genomics/halo/blob/main/LICENSE) file for more details.\n\nCredits\n-------\n[HTSlib](https://github.com/samtools/htslib) is heavily used for all genomic alignment variant processing. [Boost](https://www.boost.org/) for various data structures and algorithms.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgear-genomics%2Fhalo","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgear-genomics%2Fhalo","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgear-genomics%2Fhalo/lists"}