https://github.com/rnabioco/fcount-rs

Rust-based exon counting optimized for RNA-seq
https://github.com/rnabioco/fcount-rs

featurecounts rna-seq

Last synced: 2 months ago
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Rust-based exon counting optimized for RNA-seq

• Host: GitHub
• URL: https://github.com/rnabioco/fcount-rs
• Owner: rnabioco
• License: mit
• Created: 2025-12-31T16:44:35.000Z (5 months ago)
• Default Branch: main
• Last Pushed: 2026-03-27T12:26:04.000Z (3 months ago)
• Last Synced: 2026-03-27T23:29:29.056Z (3 months ago)
• Topics: featurecounts, rna-seq
• Language: Rust
• Homepage: https://rnabioco.github.io/fcount-rs/
• Size: 1.25 MB
• Stars: 1
• Watchers: 0
• Forks: 0
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# fcount-rs

[![CI](https://github.com/rnabioco/fcount-rs/actions/workflows/ci.yml/badge.svg)](https://github.com/rnabioco/fcount-rs/actions/workflows/ci.yml)

[![Docs](https://img.shields.io/badge/docs-mkdocs-blue)](https://rnabioco.github.io/fcount-rs)

[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)

**🚧 fcount-rs is under active development. Caveat emptor. 🚧**

Ultrafast feature counting for RNA-seq data. A high-performance Rust alternative to featureCounts.

## Performance

fcount-rs is significantly faster than featureCounts, especially with multiple threads:

| Command | Mean [s] | Relative |

|:---|---:|---:|

| featureCounts (1 thread) | 2.41 ± 0.01 | 7.67× slower |

| featureCounts (8 threads) | 0.84 ± 0.01 | 2.68× slower |

| fcount-rs (1 thread) | 1.16 ± 0.02 | 3.70× slower |

| **fcount-rs (8 threads)** | **0.31 ± 0.01** | **1.00** |

*Benchmark: chr22 subset (~1.4M paired-end reads), measured with [hyperfine](https://github.com/sharkdp/hyperfine). featureCounts v2.0.6, Subread.*

## Installation

```bash

cargo install fcount-rs

```

Or build from source:

```bash

git clone https://github.com/rnabioco/fcount-rs

cd fcount-rs

cargo build --release

```

## Usage

```bash

# Basic usage

fcount -a annotation.gtf -o counts.txt sample.bam

# Paired-end mode

fcount -a annotation.gtf -o counts.txt -p sample.bam

# Multiple samples with custom names

fcount -a annotation.gtf -o counts.txt -p control=ctrl.bam treated=treat.bam

# With 8 threads, strand-specific, primary alignments only

fcount -a annotation.gtf -o counts.txt -p -t 8 -s 2 --primary sample.bam

```

### Key Options

```

Input/Output:

  -a, --annotation     GTF/GFF annotation file

  -o, --output        Output count matrix file

Paired-End:

  -p, --paired              Count fragments instead of reads

  -B, --both-aligned        Require both ends aligned

  -C, --no-chimeric         Exclude chimeric fragments

Filtering:

  -Q, --min-mapq       Minimum mapping quality [default: 0]

  --primary                 Count primary alignments only

  --ignore-dup              Ignore duplicate reads

Strandedness:

  -s, --strand        0=unstranded, 1=stranded, 2=reversely stranded [default: 0]

Multi-mapping:

  -M, --multi-mapping       Count multi-mapping reads

  --fraction                Fractional counting (1/NH) for multi-mappers

Overlap:

  -O, --multi-overlap       Allow reads to overlap multiple features

  --min-overlap        Minimum overlapping bases [default: 1]

  --largest-overlap         Assign to feature with largest overlap

Performance:

  -t, --threads        Number of threads (0 = auto) [default: 0]

```

See the [full documentation](https://rnabioco.github.io/fcount-rs) for all options and examples.

## License

MIT