# alexdobin/STAR

RNA-seq aligner

Repository: https://github.com/alexdobin/STAR
Canonical: https://ross.abutalabs.com/products/star
Language: C
License: MIT
License Family: permissive
Last push: 2025-03-18T01:34:34+00:00

## Health v2 (maintenance only)
Score: 28/100 (v2, computed 2026-09-03T02:20:16.233290+00:00)
- activity 11, release rhythm 8, longevity 100
- inputs: {"age_days": 4554, "days_push": 534, "days_rel": null, "gap_med": null, "n_releases_24m": 0}
- flags: none
- formula: round(0.45*activity + 0.35*rhythm + 0.20*longevity); archived -> min(score, 10)

## Adoption (not part of the score)
Stars 2241, forks 550 (observed 2026-08-28T04:06:29.703680+00:00)

## What it is
STAR (Spliced Transcripts Alignment to a Reference) is a fast, splice-aware aligner for RNA-seq reads written in C++. It aligns reads to a reference genome, detecting splice junctions and producing alignments for downstream transcript quantification.

## Use cases
- align RNA-seq reads to a reference genome
- detect splice junctions in transcriptomic data
- generate alignments for gene expression quantification
- process bulk RNA-seq FASTQ files
- build a genome index for spliced alignment

## When to choose
- you need a fast, accurate splice-aware aligner for RNA-seq data
- you are running a standard bulk RNA-seq pipeline (e.g., with featureCounts, RSEM, or DESeq2 downstream)
- you have sufficient RAM (tens of GB) to hold a pre-built genome index
- you want a widely used, well-validated tool with an active community

## When to avoid
- you are aligning small RNA-seq or very short reads where specialized aligners may be better suited
- your machine has limited memory, since STAR's genome index can require large amounts of RAM
- you need a cloud-native or GUI-based tool rather than a command-line executable
- you are working on Windows natively, as pre-built binaries target Linux and macOS

## Facets
- artifact type: cli-tool
- maturity: active
- function: parser, search-engine, developer-tools
- domain: bioinformatics
- platform: cli, cpp
- tags: rna-seq, splice-aware-alignment, genomics, bioinformatics, sequence-alignment, transcriptomics, command-line, linux, macos

## Member repositories
- alexdobin/STAR (main) score 28

## Provenance
- Observed fields: from GitHub, fetched 2026-08-28T04:06:29.703680+00:00.
- Health v2: computed from the inputs above; adoption is never an input.
- Inferred fields (summary, facets, guidance): AI-extracted, prompt v1, taxonomy v1, on 2026-08-30T02:44:06.199389+00:00, confidence not recorded.
  - readme: https://github.com/alexdobin/STAR (fetched 2026-08-28T04:06:29.703680+00:00, sha 2d18b53503ee)
- Data as of 2026-08-30T08:39:29.467469+00:00.