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rustar-aligner v0.1.0

Introduction

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

It aims to be a faithful port of STAR. That means:

  • The same genome index format on disk
  • The same --camelCase command-line parameters
  • SAM/BAM output that matches STAR’s byte-for-byte where the algorithm is deterministic, and is provably equivalent (same alignment set, different tie-break) where it isn’t

If you have a STAR-based pipeline, you can swap the binary and the rest of the pipeline doesn’t need to know.

Why a Rust port?

Section titled “Why a Rust port?”

The original STAR is excellent, battle-tested, and unlikely to be replaced. rustar-aligner exists to:

  • Bring STAR’s behaviour to a memory-safe toolchain with modern dependencies
  • Provide a maintainable base for future RNA-seq alignment work that diverges from STAR (new features, different tradeoffs)
  • Verify, by reimplementing it, that STAR’s algorithms and thresholds are well-understood — every divergence found in the process becomes a documented edge case rather than a mystery

What’s supported today

Section titled “What’s supported today”

End-to-end RNA-seq alignment with all of the features most pipelines need:

  • Single-end and paired-end alignment with mate rescue
  • SAM, unsorted BAM, and coordinate-sorted BAM output
  • 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 — 4-tier pipeline including multi-junction Tier 3
  • Gene-level read counting (--quantMode GeneCounts)
  • Transcriptome-coordinate SAM output (--quantMode TranscriptomeSAM)
  • Splice junction output (SJ.out.tab)
  • Unmapped read output to FASTQ
  • Gzip-compressed FASTQ input
  • Read group tags (--outSAMattrRGline)
  • Seeded RNG for reproducible tie-breaking (--runRNGseed)
  • All the standard SAM optional tags: NH, HI, AS, NM, nM, XS, jM, jI, MD
  • Log.final.out statistics file (STAR-compatible, MultiQC-parseable)

See the STAR compatibility report for the detailed alignment-by-alignment comparison.

What’s not yet there

Section titled “What’s not yet there”
  • STARsolo single-cell features

Project status

Section titled “Project status”

rustar-aligner is the result of a phased reimplementation of STAR’s algorithms in Rust. It’s reached behavioural parity for the core alignment pipeline; the test suite (396 tests, 0 clippy warnings) plus a yeast differential-testing benchmark against STAR 2.7.x keeps it honest. Most of the code was written by Claude Code under direction from the project maintainer.

The codebase is licensed MIT (matching STAR’s license).

Where to next

Section titled “Where to next”