{"id":16755312,"url":"https://github.com/ebedthan/sabreur","last_synced_at":"2025-09-15T08:44:17.094Z","repository":{"id":57666160,"uuid":"357672732","full_name":"Ebedthan/sabreur","owner":"Ebedthan","description":"fast, reliable and handy demultiplexing tool for fastx files","archived":false,"fork":false,"pushed_at":"2024-04-02T15:57:49.000Z","size":63675,"stargazers_count":14,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-03-18T05:51:20.426Z","etag":null,"topics":["bioinformatics","demultiplexing","rust","sequence-analysis"],"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/Ebedthan.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":"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}},"created_at":"2021-04-13T19:55:32.000Z","updated_at":"2024-04-01T10:21:06.000Z","dependencies_parsed_at":"2022-09-24T04:43:34.451Z","dependency_job_id":"2680185a-4576-41cc-beda-d1e1a137b322","html_url":"https://github.com/Ebedthan/sabreur","commit_stats":{"total_commits":136,"total_committers":1,"mean_commits":136.0,"dds":0.0,"last_synced_commit":"285e4ae76c113b5857c9ecc68a7ff0db5930fb8b"},"previous_names":[],"tags_count":8,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Ebedthan%2Fsabreur","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Ebedthan%2Fsabreur/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Ebedthan%2Fsabreur/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Ebedthan%2Fsabreur/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Ebedthan","download_url":"https://codeload.github.com/Ebedthan/sabreur/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":244885013,"owners_count":20526282,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","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","demultiplexing","rust","sequence-analysis"],"created_at":"2024-10-13T03:07:19.711Z","updated_at":"2025-09-15T08:44:17.069Z","avatar_url":"https://github.com/Ebedthan.png","language":"Rust","readme":"# sabreur\n\n\u003cp align=\"center\"\u003e\n  \u003ca href=\"https://github.com/Ebedthan/sabreur/actions/workflows/ci.yml\"\u003e\n    \u003cimg alt=\"CI\" src=\"https://github.com/Ebedthan/sabreur/actions/workflows/ci.yml/badge.svg\"\u003e\n  \u003c/a\u003e\n  \u003ca href=\"https://codecov.io/gh/Ebedthan/sabreur\"\u003e\n    \u003cimg alt=\"Coverage\" src=\"https://codecov.io/gh/Ebedthan/sabreur/branch/main/graph/badge.svg\"\u003e\n  \u003c/a\u003e\n  \u003ca href=\"https://github.com/Ebedthan/sabreur\"\u003e\n    \u003cimg alt=\"Rust version\" src=\"https://img.shields.io/badge/rust-1.78.0%2B-blue.svg?maxAge=3600\"\u003e\n  \u003c/a\u003e\n  \u003ca href=\"https://github.com/Ebedthan/sabreur/blob/master/LICENSE\"\u003e\n    \u003cimg alt=\"License\" src=\"https://img.shields.io/badge/license-MIT-blue?style=flat\"\u003e\n  \u003c/a\u003e\n\u003c/p\u003e\n\n\u003cp align=\"center\"\u003e\n  \u003cimg src=\"img/sabreur.png\" alt=\"sabreur logo\" width=\"150\"\u003e\n\u003c/p\u003e\n\n## 🔎 About\n\n**sabreur** is a command-line tool designed to **demultiplex barcoded sequencing reads** into separate files. It supports:\n\n- **FASTA** and **FASTQ** formats\n- **Compressed inputs and outputs**: `gzip`, `bzip2`, `xz`, and `zstd`\n- **Paired-end** and **Single-end** reads\n\nIt uses a barcode file to match reads and dispatches each to the corresponding output. Reads with unknown barcodes go into a separate file.\n\nPowered by [niffler](https://github.com/luizirber/niffler) for seamless compression support.\n\n## 🚀 Usage\n\n### ▶️ Paired-end mode\n\n```bash\nsabreur barcode.txt input_R1.fq.gz input_R2.fq.gz\n```\n### ▶️ Single-end mode\n```bash\nsabreur barcode.txt input.fq\n```\n\nsabreur automatically detects the format and compression. Just provide the inputs!\n\n## ⚙️ Command-Line Options\n```\nUSAGE:\n    sabreur [options] \u003cBARCODE\u003e \u003cFORWARD FILE\u003e [\u003cREVERSE FILE\u003e]\n\nARGS:\n    \u003cBARCODE\u003e    input barcode file\n    \u003cFORWARD\u003e    input forward fastx file\n    \u003cREVERSE\u003e    input reverse fastx file\n\nOPTIONS:\n    -m, --mismatch \u003cINT\u003e    maximum number of mismatches [default: 0]\n    -o, --out \u003cDIR\u003e         ouput directory [default: sabreur_out]\n    -f, --format \u003cSTR\u003e      output files compression format\n    -l, --level \u003cINT\u003e       compression level [default: 1]\n        --force             force reuse of output directory\n    -q, --quiet             decrease program verbosity\n    -h, --help              Print help information\n    -V, --version           Print version information\n\n```\n\n## 📦 Installation\n\n### Requirements\n- [Rust](https://rust-lang.org) in stable channel\n- libgz for gz file support\n- liblzma for xz file support\n- libbzip2 for bzip2 file support\n- zstd for zstd file support\n\n### 🛠️ From Source (via Cargo)\n\n```bash\ngit clone https://github.com/Ebedthan/sabreur.git\ncd sabreur\ncargo install --path . --root ~/.cargo\nsabreur --help\n```\n\n### 📁 Prebuilt Binaries\n\nDownload binaries for your platform from the [releases page](https://github.com/Ebedthan/sabreur/releases):\n\n* macOS (Apple Silicon): [Download](https://github.com/Ebedthan/sabreur/releases/download/v0.7.0/sabreur-v0.7.0-aarch64-apple-darwin.tar.xz) • [Checksum](https://github.com/Ebedthan/sabreur/releases/download/v0.7.0/sabreur-v0.7.0-aarch64-apple-darwin.tar.xz.sh256)\n* macOS (Intel): [Download](https://github.com/Ebedthan/sabreur/releases/download/v0.7.0/sabreur-v0.7.0-x86_64-apple-darwin.tar.xz) • [Checksum](https://github.com/Ebedthan/sabreur/releases/download/v0.7.0/sabreur-v0.7.0-x86_64-apple-darwin.tar.xz.sha256)\n* Linux (x86\\_64): [Download](https://github.com/Ebedthan/sabreur/releases/download/v0.7.0/sabreur-v0.7.0-x86_64-unknown-linux-gnu.tar.xz) • [Checksum](https://github.com/Ebedthan/sabreur/releases/download/v0.7.0/sabreur-v0.7.0-x86_64-unknown-linux-gnu.tar.xz.sha256)\n* Windows (x86\\_64): [Download](https://github.com/Ebedthan/sabreur/releases/download/v0.7.0/sabreur-v0.7.0-x86_64-pc-windows-msvc.zip) • [Checksum](https://github.com/Ebedthan/sabreur/releases/download/v0.7.0/sabreur-v0.7.0-x86_64-pc-windows-msvc.zip.sha256)\n\n## Benchmark\n\nBenchmarked with [hyperfine](https://github.com/sharkdp/hyperfine) [dataset](https://figshare.com/articles/dataset/Paired-end_fastq_files_for_demultiplexing/14701629).\n\n\n| Tool  | Single-end uncompressed output | Single-end compressed output | Paired-end uncompressed output | Paired-end compressed output |\n| :---  |             :----:             |             :----:           |              :----:           |              :----:           |\n| [idemp](https://github.com/yhwu/idemp) | - | 211.571 ± 3.718 | -      | 366.247 ± 10.482  |\n| [sabre](https://github.com/najoshi/sabre) | 32.911 ± 2.411 | - | 109.470 ± 49.909 | -     |\n| **sabreur** | 10.843 ± 0.531| 93.840 ± 0.446    | 40.878 ± 13.743     | 187.533 ± 0.572   |\n\n\n### 🗜️ Compression format performance\n\nA simple benchmark of the different compression format (`sabreur tests/bc_pe_fq.txt tests/input_R1.fastq.gz tests/input_R2.fastq.gz`), zst being the fastest.\n\n| Command | Mean [s] | Min [s] | Max [s] | Relative |\n|:---|---:|---:|---:|---:|\n| `--format zst` | 43.096 ± 1.547 | 41.179 | 46.878 | 1.00 |\n| `--format bz2` | 94.049 ± 4.762 | 87.984 | 101.140 | 2.18 ± 0.14 |\n| `--format gz` | 123.107 ± 1.748 | 120.529 | 125.166 | 2.86 ± 0.11 |\n| `--format xz` | 285.692 ± 18.625 | 264.960 | 325.750 | 6.63 ± 0.49 |\n\n\n## 📄 Barcode File Format\n\nThe barcode file must be tab-delimited in the format:\n\n```\nbarcode1    barcode1_file1.fq   barcode1_file2.fq\nbarcode2    barcode2_file1.fq   barcode2_file2.fq\n...\n```\n\nOutput filenames must be unique. You can use .fq, .fastq, .fa, or .fasta as extensions.\n\n### Minimum supported Rust version\n`sabreur` minimum [Rust](https://www.rust-lang.org/) version is 1.78.0.\n\n## 🤝 Contributing\n\n- Contributions are welcome under the [Contributor Code of Conduct](https://github.com/Ebedthan/sabreur/blob/main/CODE_OF_CONDUCT.md).\n- Please open an [issue or pull request on GitHub](https://github.com/Ebedthan/sabreur/issues).\n\n## 🐛 Bugs \u0026 Support\n\nFound a bug or have a feature request? → [Open an issue](https://github.com/Ebedthan/sabreur/issues).\n\n## 📜 License\nThis project is licensed under the MIT License.\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Febedthan%2Fsabreur","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Febedthan%2Fsabreur","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Febedthan%2Fsabreur/lists"}