https://github.com/scverse/rustar-aligner

A rust implementation of STAR
https://github.com/scverse/rustar-aligner

Last synced: 14 days ago
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A rust implementation of STAR

• Host: GitHub
• URL: https://github.com/scverse/rustar-aligner
• Owner: scverse
• License: mit
• Created: 2026-02-06T05:20:41.000Z (4 months ago)
• Default Branch: main
• Last Pushed: 2026-05-12T12:37:43.000Z (26 days ago)
• Last Synced: 2026-05-12T14:32:57.400Z (26 days ago)
• Language: Rust
• Homepage: https://scverse.org/rustar-aligner/
• Size: 2.84 MB
• Stars: 39
• Watchers: 1
• Forks: 2
• Open Issues: 4
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE
  • Roadmap: ROADMAP.md

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README

          
# ![rustar-aligner](docs/src/assets/rustar-logo.svg)

A Rust reimplementation of [STAR](https://github.com/alexdobin/STAR) (Spliced Transcripts Alignment to a Reference), the widely-used RNA-seq aligner originally written in C++ by Alexander Dobin.

## Overview

rustar-aligner aims to be a faithful port of STAR, matching the original behavior as closely as possible. It uses the same genome index format, accepts the same `--camelCase` command-line parameters, and produces compatible SAM/BAM output.

**Current status**: End-to-end single-end and paired-end RNA-seq alignment with splice junction detection, two-pass mode, chimeric alignment detection (including multi-junction Tier 3), gene-level quantification, and multi-threaded parallel processing. 396 tests passing (383 unit + 8 integration + others), 0 clippy warnings.

## Quick Start

### Build

```bash

cargo build --release

```

### Generate genome index

```bash

target/release/rustar-aligner --runMode genomeGenerate \

  --genomeDir /path/to/genome_index \

  --genomeFastaFiles /path/to/genome.fa

```

### Align reads

```bash

target/release/rustar-aligner \

  --genomeDir /path/to/genome_index \

  --readFilesIn reads.fq \

  --outSAMtype SAM \

  --outSAMstrandField intronMotif \

  --outFileNamePrefix /path/to/output_

```

### Paired-end alignment

```bash

target/release/rustar-aligner \

  --genomeDir /path/to/genome_index \

  --readFilesIn reads_1.fq reads_2.fq \

  --outSAMtype SAM \

  --outFileNamePrefix /path/to/output_

```

### BAM output

```bash

target/release/rustar-aligner \

  --genomeDir /path/to/genome_index \

  --readFilesIn reads.fq \

  --outSAMtype BAM Unsorted \

  --outFileNamePrefix /path/to/output_

```

### Coordinate-sorted BAM output

```bash

target/release/rustar-aligner \

  --genomeDir /path/to/genome_index \

  --readFilesIn reads.fq \

  --outSAMtype BAM SortedByCoordinate \

  --outFileNamePrefix /path/to/output_

```

### Two-pass mode

```bash

target/release/rustar-aligner \

  --genomeDir /path/to/genome_index \

  --readFilesIn reads.fq \

  --twopassMode Basic \

  --outFileNamePrefix /path/to/output_

```

### Gene-level counts

```bash

target/release/rustar-aligner \

  --genomeDir /path/to/genome_index \

  --readFilesIn reads.fq \

  --sjdbGTFfile /path/to/annotation.gtf \

  --quantMode GeneCounts \

  --outFileNamePrefix /path/to/output_

```

## Accuracy Comparison vs STAR

Benchmarked on 10,000 yeast RNA-seq reads (150 bp, ERR12389696), compared to STAR 2.7.x with identical parameters and genome index.

### Single-End (10k reads, 150 bp SE)

| Metric | rustar-aligner | STAR |

|--------|----------------|------|

| Unique mapped | 82.6% | 82.6% |

| Multi-mapped | 7.4% | 7.4% |

| Total mapped | 90.0% | 90.0% |

| Position agreement | 96.5% raw / **99.815% tie-adjusted** | — |

| STAR-only reads | **0** | — |

| rustar-aligner-only reads | **0** | — |

| CIGAR-only diffs | 1 (seed-level tie in homopolymer) | — |

> **Tie-adjusted**: 299 of 313 disagreements are verified genuine ties — both tools find identical alignment sets but select different copies due to SA-order or RNG tie-breaking differences. Excluding these, faithfulness is 99.815% (8,611/8,627 non-tie reads exact).

### Paired-End (10k read pairs, 150 bp)

| Metric | rustar-aligner | STAR |

|--------|----------------|------|

| Both mates mapped | **8,390** | 8,390 |

| Half-mapped pairs | **0** | 0 |

| Unmapped pairs | 0 | 0 |

| PE faithfulness (tie-adjusted) | **99.883%** | — |

| MAPQ inflations | **0** | — |

| MAPQ deflations | **0** | — |

| NH tag diffs | **0** | — |

| Proper-pair diffs | **0** | — |

> **PE faithfulness**: 16,284 / 16,306 mate alignments exactly match STAR (same position, CIGAR, MAPQ, proper-pair flag, and NH tag). 475 diffs excluded as tie-breaking differences (same MAPQ+NH, different repeat copy chosen).

## Supported Features

- Single-end and paired-end alignment with mate rescue

- SAM, unsorted BAM, and coordinate-sorted BAM output (`--outSAMtype SAM`, `BAM Unsorted`, or `BAM SortedByCoordinate`)

- Multi-threaded parallel alignment (`--runThreadN`)

- GTF-based junction annotation with scoring bonus (`--sjdbGTFfile`)

- Two-pass mode for novel junction discovery (`--twopassMode Basic`)

- SJDB insertion into genome index at genomeGenerate time

- Chimeric alignment detection — SE and PE, 4-tier pipeline: transcript-pair search, multi-cluster, soft-clip re-seeding, residual outer re-seeding for multi-junction fusions (`--chimSegmentMin`)

- Gene-level read counting (`--quantMode GeneCounts` → `ReadsPerGene.out.tab`)

- Transcriptome-coordinate SAM output (`--quantMode TranscriptomeSAM`)

- Post-alignment read filtering (`--outFilterType BySJout`)

- Splice junction output (`SJ.out.tab`)

- Unmapped read output to FASTQ (`--outReadsUnmapped Fastx` → `Unmapped.out.mate1` / `mate2`)

- Gzip-compressed FASTQ input (`--readFilesCommand zcat`)

- Read group tags (`--outSAMattrRGline`)

- Seeded RNG for reproducible tie-breaking (`--runRNGseed`)

- SAM optional tags: NH, HI, AS, NM, nM, XS, jM, jI, MD

- `--outSAMattributes` control (Standard/All/None/explicit list)

- SECONDARY flag (0x100) on multi-mapper alignments

- Configurable output limits (`--outSAMmultNmax`)

- Bidirectional seed search with `scoreSeedBest` pre-extension

- Junction boundary optimization (jR scanning)

- Log.final.out statistics file (STAR-compatible, MultiQC-parseable)

## Known Limitations

- No STARsolo single-cell features (Phase 14, deferred)

See [ROADMAP.md](ROADMAP.md) for detailed implementation tracking.

## Building from Source

Requires Rust 2024 edition (rustc 1.85+).

```bash

cargo build --release       # Release build

cargo test                  # Run tests

cargo clippy --all-targets  # Lint

cargo fmt                   # Format

```

## Development

The majority of rustar-aligner's code was written by [Claude Code](https://claude.ai/code) (Anthropic's AI coding assistant), with technical direction, architecture decisions, and validation by the project maintainer.

## License

MIT (matching the original STAR license)