# Installer stringtie avec Homebrew, apt Consultez les chemins d'installation, exécutables, métadonnées et notes de sécurité de stringtie pour les workflows d'agents IA. ## installation ```sh sudo av install brew:stringtie ``` Commandes d'installation supplémentaires: ### macOS - Homebrew (100%): ```sh brew install stringtie ``` Preuve: local Homebrew formula metadata ### Linux - Debian apt (92%): ```sh sudo apt install stringtie ``` Preuve: Debian stable package indexes: stringtie from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz ## Faits du paquet - **Clé du paquet:** brew:stringtie - **Gestionnaire de paquets:** Homebrew - **Page du gestionnaire de paquets:** - **Version:** 3.0.3 - **Résumé source:** Transcript assembly and quantification for RNA-Seq - **Page d'accueil:** - **Dépôt:** - **Licence:** MIT - **Archive source:** - **Dernière mise à jour:** 2026-06-22T14:06:23-07:00 - **Généré:** 2026-08-04T22:13:35+00:00 ## exécutables - stringtie (cli) - stringtie (alias) ## Dépendances - htslib ## Comportement d'installation - hook post-installation: non défini - Bouteille: disponible sur arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux ## Version et fraîcheur - page générée: 2026-08-04 - version du gestionnaire: 3.0.3 - gestionnaire mis à jour: 2026-06-22 - données locales: OK - dépôt amont: https://github.com/gpertea/stringtie - dernière version détectée: v3.0.3 (à jour) ## Historique du projet et usages 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. ### Historique du projet 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. ### Historique d'adoption 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. ### Modes d'utilisation 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. ### Pourquoi les passionnés de paquets s'y intéressent 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. ### Chronologie - 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. ### Sources - - - - source_facts.package-manager ## Notes de sécurité narrow executable package without higher-risk signals. - **Risque Geiger:** vert / faible - narrow executable package without higher-risk signals ## Détails de la base source - **Source Database:** Homebrew formula API - **Tap:** homebrew/core - **Full Name:** stringtie - **Version Scheme:** 0 - **Revision:** 0 - **Head Version:** HEAD - **Bottle Stable Root URL:** - **Deprecated:** no - **Disabled:** no - **Keg Only:** no - **URL Keys:** head, stable ## Autres enregistrements de gestionnaires de paquets - 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/ ## Liens liés - [Source-control packages](https://pkg.so/fr/source-control-tools/) - Belongs to a source-control command family. - [Terminal utility packages](https://pkg.so/fr/terminal-utilities/) - Matched terminal and command-line workflow metadata. - [Networking and protocol packages](https://pkg.so/fr/networking-protocol-tools/) - Matched network, protocol, or remote-service metadata. - [Scientific computing packages](https://pkg.so/fr/scientific-computing-tools/) - Matched scientific computing metadata. - [htslib](https://pkg.so/fr/brew/htslib/) - Runtime dependency declared by Homebrew. - [salmon](https://pkg.so/fr/brew/salmon/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, quantification, rna-seq. - [kallisto](https://pkg.so/fr/brew/kallisto/) - Shares pkgdb curated category or tags: bioinformatics, cli, quantification, rna-seq, science. - [rna-star](https://pkg.so/fr/brew/rna-star/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, rna-seq, science. - [samtools](https://pkg.so/fr/brew/samtools/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science. - [blast](https://pkg.so/fr/brew/blast/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science. - [bedtools](https://pkg.so/fr/brew/bedtools/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science. - [minimap2](https://pkg.so/fr/brew/minimap2/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science. - [oarfish](https://pkg.so/fr/brew/oarfish/) - Local package facts share a topical domain. Shared terms: bioinformatics, cli, quantification, rna, rna-seq. ## Combined YAML source View the package source record on GitHub. [combined/stringtie.yml](https://github.com/mxcl/pkgdb/blob/main/combined/stringtie.yml) ## Sources - pkg.so package database - Geiger risk classifier - package-page enrichment - curated package history - package version freshness - pkgdb category and tag curation - package relationship graph - external package-manager database matches - cross-ecosystem install command graph