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Caveat emptor. 🚧**\n\nUltrafast feature counting for RNA-seq data. A high-performance Rust alternative to featureCounts.\n\n## Performance\n\nfcount-rs is significantly faster than featureCounts, especially with multiple threads:\n\n| Command | Mean [s] | Relative |\n|:---|---:|---:|\n| featureCounts (1 thread) | 2.41 ± 0.01 | 7.67× slower |\n| featureCounts (8 threads) | 0.84 ± 0.01 | 2.68× slower |\n| fcount-rs (1 thread) | 1.16 ± 0.02 | 3.70× slower |\n| **fcount-rs (8 threads)** | **0.31 ± 0.01** | **1.00** |\n\n*Benchmark: chr22 subset (~1.4M paired-end reads), measured with [hyperfine](https://github.com/sharkdp/hyperfine). featureCounts v2.0.6, Subread.*\n\n## Installation\n\n```bash\ncargo install fcount-rs\n```\n\nOr build from source:\n\n```bash\ngit clone https://github.com/rnabioco/fcount-rs\ncd fcount-rs\ncargo build --release\n```\n\n## Usage\n\n```bash\n# Basic usage\nfcount -a annotation.gtf -o counts.txt sample.bam\n\n# Paired-end mode\nfcount -a annotation.gtf -o counts.txt -p sample.bam\n\n# Multiple samples with custom names\nfcount -a annotation.gtf -o counts.txt -p control=ctrl.bam treated=treat.bam\n\n# With 8 threads, strand-specific, primary alignments only\nfcount -a annotation.gtf -o counts.txt -p -t 8 -s 2 --primary sample.bam\n```\n\n### Key Options\n\n```\nInput/Output:\n  -a, --annotation \u003cGTF\u003e    GTF/GFF annotation file\n  -o, --output \u003cFILE\u003e       Output count matrix file\n\nPaired-End:\n  -p, --paired              Count fragments instead of reads\n  -B, --both-aligned        Require both ends aligned\n  -C, --no-chimeric         Exclude chimeric fragments\n\nFiltering:\n  -Q, --min-mapq \u003cINT\u003e      Minimum mapping quality [default: 0]\n  --primary                 Count primary alignments only\n  --ignore-dup              Ignore duplicate reads\n\nStrandedness:\n  -s, --strand \u003cMODE\u003e       0=unstranded, 1=stranded, 2=reversely stranded [default: 0]\n\nMulti-mapping:\n  -M, --multi-mapping       Count multi-mapping reads\n  --fraction                Fractional counting (1/NH) for multi-mappers\n\nOverlap:\n  -O, --multi-overlap       Allow reads to overlap multiple features\n  --min-overlap \u003cINT\u003e       Minimum overlapping bases [default: 1]\n  --largest-overlap         Assign to feature with largest overlap\n\nPerformance:\n  -t, --threads \u003cINT\u003e       Number of threads (0 = auto) [default: 0]\n```\n\nSee the [full documentation](https://rnabioco.github.io/fcount-rs) for all options and examples.\n\n## License\n\nMIT\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frnabioco%2Ffcount-rs","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Frnabioco%2Ffcount-rs","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frnabioco%2Ffcount-rs/lists"}