# stringtie mit Homebrew, apt installieren

Prüfe Installationswege, Executables, Metadaten und Sicherheitshinweise für stringtie in AI-Agent-Workflows.

## Installation

```sh
sudo av install brew:stringtie
```

Weitere Installationsbefehle:

### macOS

- Homebrew (100%):

```sh
brew install stringtie
```

  Evidenz: local Homebrew formula metadata

### Linux

- Debian apt (92%):

```sh
sudo apt install stringtie
```

  Evidenz: Debian stable package indexes: stringtie from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz

## Paketfakten

- **Paketschlüssel:** brew:stringtie
- **Paketmanager:** Homebrew
- **Version:** 3.0.3
- **Quellzusammenfassung:** Transcript assembly and quantification for RNA-Seq
- **Homepage:** <https://github.com/gpertea/stringtie>
- **Repository:** <https://github.com/gpertea/stringtie>
- **Zuletzt aktualisiert:** 2026-06-22T14:06:23-07:00
- **Generiert:** 2026-08-03T19:37:03+00:00

## Executables

- stringtie (Alias)

## Installationsverhalten

- Bottle: nicht verfügbar

## Version und Aktualität

- Seite generiert: 2026-08-03
- Manager-Version: 3.0.3
## Projektgeschichte und Nutzung

StringTie is a bioinformatics CLI for transcript assembly and quantification from RNA-Seq alignments, packaged for command-line genomics workflows rather than general developer tooling.

### Projektgeschichte

The official Johns Hopkins CCB page describes StringTie as a fast assembler of RNA-Seq alignments into potential transcripts, using a network-flow algorithm and optional de novo assembly. The project README points users to the CCB site as the official documentation and source/binary package surface.

The CCB publication list anchors the project in the 2015 Nature Biotechnology paper introducing StringTie for improved transcriptome reconstruction from RNA-Seq reads. Later official release notes show the tool evolving through StringTie2 long-read support and StringTie3 features such as nascent-aware assembly.

### Adoptionsgeschichte

StringTie became part of the command-line genomics stack alongside aligners and downstream expression tools. The official manual describes input from sorted SAM/BAM/CRAM alignments and mentions common upstream aligners such as TopHat, HISAT2, STAR, and minimap2.

The supplied package-manager facts show Homebrew, Debian, and Ubuntu packaging, which matters for bioinformatics users who install complete pipelines on workstations, clusters, and reproducible analysis environments.

### Wie es verwendet wird

Typical use is `stringtie [-o output.gtf] [options] read_alignments.bam`, producing GTF transcript structures and expression values. The manual documents reference-guided assembly, merge mode, expression-estimation mode, long-read mode, mixed short/long-read mode, and outputs for downstream differential-expression tools.

Package users care about the CLI because it composes cleanly with samtools, HISAT2, STAR, minimap2, Ballgown, DESeq2, edgeR, and workflow managers without requiring a graphical environment.

### Warum Paket-Nerds sich dafür interessieren

StringTie is a good example of a scientific binary that package managers keep useful by standardizing installation across macOS and Linux, especially when users need reproducible pipelines rather than hand-built lab software.

It also shows why package metadata matters in science: the same executable name, docs, license, and source repository need to be discoverable across brew, Debian-family systems, and workflow recipes.

### Zeitleiste

- 2014-10-13: GitHub repository metadata records public repository creation.
- 2015: CCB publication list cites the Nature Biotechnology paper introducing StringTie.
- 2019: CCB publication list cites StringTie2 for transcriptome assembly from long-read RNA-seq alignments.
- 2021: Official release notes describe StringTie 2.2.0 support for mixed short- and long-read alignments and CRAM input.
- 2025: Official release notes describe StringTie 3.0.0 and nascent-aware assembly work.

### Related projects

- HISAT2, TopHat, STAR, minimap2, samtools, Ballgown, DESeq2, edgeR, gffcompare, and GFF utilities are adjacent tools named by the official docs or workflow context.

### Quellen

- <https://ccb.jhu.edu/software/stringtie>
- <https://ccb.jhu.edu/software/stringtie/index.shtml?t=manual>
- <https://github.com/gpertea/stringtie#readme>
- source_facts.package-manager


## Sicherheitshinweise

narrow executable package without higher-risk signals.

- **Geiger-Risiko:** grün / niedrig
- narrow executable package without higher-risk signals

## Andere Paketmanager-Einträge

- Debian apt - stringtie - 2.2.1+ds-3+b1: normalized package name match | Debian stable package indexes: stringtie from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | assemble short RNAseq reads to transcripts | https://ccb.jhu.edu/software/stringtie/
- Ubuntu apt - stringtie - 2.2.1+ds-3build2: normalized package name match | Ubuntu 24.04 LTS package indexes: stringtie from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | assemble short RNAseq reads to transcripts | https://ccb.jhu.edu/software/stringtie/


## Combined YAML source

View the package source record on GitHub. [combined/stringtie.yml](https://github.com/mxcl/pkgdb/blob/main/combined/stringtie.yml)


## Quellen

- pkg.so package database
- Geiger risk classifier
- curated package history
- pkgdb category and tag curation
- external package-manager database matches
- cross-ecosystem install command graph