ruSTAR

A Rust reimplementation of STAR (Spliced Transcripts Alignment to a Reference), the widely-used RNA-seq aligner originally written in C++ by Alexander Dobin.

Overview

ruSTAR 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, and multi-threaded parallel processing. 264 tests passing.

Quick Start

Build

cargo build --release

Generate genome index

target/release/ruSTAR --runMode genomeGenerate \
  --genomeDir /path/to/genome_index \
  --genomeFastaFiles /path/to/genome.fa

Align reads

target/release/ruSTAR \
  --genomeDir /path/to/genome_index \
  --readFilesIn reads.fq \
  --outSAMtype SAM \
  --outSAMstrandField intronMotif \
  --outFileNamePrefix /path/to/output_

Paired-end alignment

target/release/ruSTAR \
  --genomeDir /path/to/genome_index \
  --readFilesIn reads_1.fq reads_2.fq \
  --outSAMtype SAM \
  --outFileNamePrefix /path/to/output_

BAM output

target/release/ruSTAR \
  --genomeDir /path/to/genome_index \
  --readFilesIn reads.fq \
  --outSAMtype BAM Unsorted \
  --outFileNamePrefix /path/to/output_

Two-pass mode

target/release/ruSTAR \
  --genomeDir /path/to/genome_index \
  --readFilesIn reads.fq \
  --twopassMode Basic \
  --outFileNamePrefix /path/to/output_

Accuracy Comparison vs STAR

Single-End (10k yeast reads, 150bp)

Alignment Rates

Metric	ruSTAR	STAR
Unique mapped	93.0%	92.6%
Multi-mapped	7.0%	7.4%
Soft-clipped reads	26.0%	26.0%
Splice rate	1.9%	2.2%

Position and CIGAR Agreement

Mode	Position agree	CIGAR agree	Splice rate
Normal (default)	97.4%	98.5%	1.9%

MAPQ Agreement

Metric	Value
MAPQ agreement	99.1%
MAPQ inflation (ruSTAR=255, STAR<255)	62 reads (was 323 pre-16.10)

Junction Statistics (SE)

Metric	ruSTAR	STAR
Shared junctions	62	72 total
ruSTAR-only junctions	0	--
Motif agreement (shared)	100%	--

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

Alignment Rates

Metric	ruSTAR	STAR
Both mates mapped	8761 (97.1%)	8390 (100%)
Half-mapped pairs	263 (2.9%)	0
Unmapped pairs	0	0

Per-Mate Agreement

Metric	Value
Per-mate position agree	97.8%
Per-mate CIGAR agree	96.0%

Junction Statistics (PE)

Metric	ruSTAR	STAR
Shared junctions	85	90 total
ruSTAR-only junctions	3	--
Motif agreement (shared)	100%	--

Note: 263 half-mapped pairs (2.9%) are cases where one mate maps but the other fails even with mate rescue. STAR uses joint DP stitching which recovers these.

Supported Features

• Single-end and paired-end alignment with mate rescue
• SAM and unsorted BAM output (--outSAMtype SAM or BAM Unsorted)
• Multi-threaded parallel alignment (--runThreadN)
• GTF-based junction annotation with scoring bonus (--sjdbGTFfile)
• Two-pass mode for novel junction discovery (--twopassMode Basic)
• Chimeric alignment detection for single-end reads (--chimSegmentMin)
• Post-alignment read filtering (--outFilterType BySJout)
• Splice junction output (SJ.out.tab)
• Gzip-compressed FASTQ input (--readFilesCommand zcat)
• SAM optional tags: NH, HI, AS, NM, nM, XS, jM, jI, MD
• --outSAMattributes control (Standard/All/None/explicit)
• SECONDARY flag (0x100) on multi-mapper alignments
• Configurable output limits (--outSAMmultNmax)
• Bidirectional seed search (L-to-R and R-to-L)
• Junction boundary optimization (jR scanning)
• Deterministic output (identical SAM across runs)
• Log.final.out statistics file (STAR-compatible, MultiQC-parseable)

Known Limitations

• No coordinate-sorted BAM output (use samtools sort post-alignment)
• No paired-end chimeric detection
• No --quantMode GeneCounts
• No --outReadsUnmapped Fastx
• No --outStd SAM/BAM (stdout output)
• Residual MAPQ inflation (~62 reads MAPQ 255 vs STAR <255) — mostly multi-mapper tie-breaking
• No STARsolo single-cell features

See ROADMAP.md for detailed implementation tracking.

Building from Source

Requires Rust 2024 edition (rustc 1.85+).

cargo build --release    # Release build
cargo test               # Run tests
cargo clippy             # Lint
cargo fmt                # Format

Development

The majority of ruSTAR's code was written by Claude Code (Anthropic's AI coding assistant), with technical direction, architecture decisions, and validation by the project maintainer.

License

MIT (matching the original STAR license)