{"id":49603083,"url":"https://github.com/codialab/gfaffix","last_synced_at":"2026-05-04T10:01:57.638Z","repository":{"id":39990726,"uuid":"382333284","full_name":"codialab/GFAffix","owner":"codialab","description":"GFAffix identifies walk-preserving shared affixes in variation graphs and collapses them into a non-redundant graph structure.","archived":false,"fork":false,"pushed_at":"2025-05-29T07:07:35.000Z","size":5947,"stargazers_count":37,"open_issues_count":2,"forks_count":5,"subscribers_count":8,"default_branch":"main","last_synced_at":"2026-02-07T19:57:48.151Z","etag":null,"topics":["gfa","handlegraph","pangenomics"],"latest_commit_sha":null,"homepage":"","language":"Rust","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/codialab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.md","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}},"created_at":"2021-07-02T12:02:39.000Z","updated_at":"2026-01-22T23:50:59.000Z","dependencies_parsed_at":"2022-08-09T15:48:16.854Z","dependency_job_id":"6598ed07-3f9a-4d1e-bc55-ab1b274840cd","html_url":"https://github.com/codialab/GFAffix","commit_stats":null,"previous_names":["codialab/gfaffix"],"tags_count":16,"template":false,"template_full_name":null,"purl":"pkg:github/codialab/GFAffix","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/codialab%2FGFAffix","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/codialab%2FGFAffix/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/codialab%2FGFAffix/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/codialab%2FGFAffix/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/codialab","download_url":"https://codeload.github.com/codialab/GFAffix/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/codialab%2FGFAffix/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":32602730,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-03T22:12:39.696Z","status":"online","status_checked_at":"2026-05-04T02:00:06.625Z","response_time":58,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"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":["gfa","handlegraph","pangenomics"],"created_at":"2026-05-04T10:01:54.414Z","updated_at":"2026-05-04T10:01:57.630Z","avatar_url":"https://github.com/codialab.png","language":"Rust","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![Rust Build](https://github.com/marschall-lab/GFAffix/actions/workflows/rust_build.yml/badge.svg)](https://github.com/marschall-lab/GFAffix/actions/workflows/rust_build.yml) [![Anaconda-Server Badge](https://anaconda.org/bioconda/gfaffix/badges/version.svg)](https://conda.anaconda.org/bioconda) [![Anaconda-Server Badge](https://anaconda.org/bioconda/gfaffix/badges/platforms.svg)](https://anaconda.org/bioconda/gfaffix) [![Anaconda-Server Badge](https://anaconda.org/bioconda/gfaffix/badges/license.svg)](https://anaconda.org/bioconda/gfaffix)\n\n# GFAffix\n\n![GFAffix collapses walk-preserving shared affixes](doc/gfaffix-illustration.png?raw=true \"GFAffix collapses walk-preserving shared affixes\")\n\nGFAffix identifies walk-preserving shared affixes in variation graphs and collapses them into a non-redundant graph structure.\n\n# Dependencies\n\n`GFAffix` is written in RUST and requires a working RUST build system for installation. See [https://www.rust-lang.org/tools/install](https://www.rust-lang.org/tools/install) for more details. \n\nIt makes use of the following crates:\n* clap\n* env\\_logger\n* flate2\n* gfa\n* handlegraph\n* indexmap\n* log\n* rayon\n* regex\n* rustc-hash\n\n## Installation\n\n### From bioconda channel\n\nMake sure you have [conda](https://conda.io)/[mamba](https://anaconda.org/conda-forge/mamba) installed!\n\n```\nmamba install -c conda-forge -c bioconda gfaffix\n```\n\n### From binary release\n\n#### Linux x86\\_64\n\n```\nwget --no-check-certificate -c https://github.com/marschall-lab/GFAffix/releases/download/0.2.2/GFAffix-0.2.2_linux_x86_64.tar.gz \ntar -xzvf GFAffix-0.2.2_linux_x86_64.tar.gz \n\n# you are ready to go! \n./GFAffix-0.2.2_linux_x86_64/gfaffix\n```\n\n#### MacOS X arm64\n\n```\nwget --no-check-certificate -c https://github.com/marschall-lab/GFAffix/releases/download/0.2.2/GFAffix-0.2.2_macos_x_arm64.tar.gz \ntar -xzvf GFAffix-0.2.2_macos_x_arm64.tar.gz \n\n# you are ready to go! \n./GFAffix-0.2.2_macos_x_arm64/gfaffix\n```\n\n### From repository\n\n```\n# install GFAffix\ngit clone https://github.com/marschall-lab/GFAffix.git\n# build program\ncargo build --manifest-path GFAffix/Cargo.toml --release\n# built binary is located at GFAffix/target/release/gfaffix\n```\n\n## Command Line Interface\n\n```\n$ gfaffix --help\nDiscover and collapse walk-preserving shared affixes of a given variation graph.\n\nUsage: gfaffix [OPTIONS] \u003cGRAPH\u003e\n\nArguments:\n  \u003cGRAPH\u003e  graph in GFA1 format, supports compressed (.gz) input\n\nOptions:\n  -o, --output_refined \u003cREFINED_GRAPH_OUT\u003e\n          Write refined graph output (GFA1 format) to supplied file instead of stdout; if file name\n          ends with .gz, output will be compressed [default: ]\n  -t, --output_transformation \u003cTRANSFORMATION_OUT\u003e\n          Report original nodes and their corresponding walks in refined graph to supplied file\n          [default: ]\n  -c, --check_transformation\n          Verifies that the transformed parts of the graphs spell out the identical sequence as in the\n          original graph\n  -a, --output_affixes \u003cAFFIXES_OUT\u003e\n          Report identified affixes [default: ]\n  -x, --dont_collapse \u003cNO_COLLAPSE_PATH\u003e\n          Do not collapse nodes on a given paths/walks (\"P\"/\"W\" lines) that match given regular\n          expression [default: ]\n  -p, --threads \u003cTHREADS\u003e\n          Run in parallel on N threads [default: 1]\n  -v, --verbose\n          Sets log level to debug\n  -h, --help\n          Print help\n  -V, --version\n          Print version\n```\n\n## Execution\n\n```\ngfaffix -c examples/example1.gfa \u003e example1.gfaffixed.gfa\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcodialab%2Fgfaffix","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcodialab%2Fgfaffix","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcodialab%2Fgfaffix/lists"}