# Install stringtie with Homebrew, apt Transcript assembly and quantification for RNA-Seq. Version 3.0.3 via Homebrew; verified 2026-06-22. ## Install ```sh sudo av install brew:stringtie ``` Additional install commands: ### macOS - Homebrew (100%): ```sh brew install stringtie ``` Evidence: local Homebrew formula metadata ### Linux - Debian apt (92%): ```sh sudo apt install stringtie ``` Evidence: Debian stable package indexes: stringtie from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz ## Package facts - **Package key:** brew:stringtie - **Package manager:** Homebrew - **Package manager page:** - **Version:** 3.0.3 - **Source summary:** Transcript assembly and quantification for RNA-Seq - **Homepage:** - **Repository:** - **Upstream docs:** - **License:** MIT - **Source archive:** - **Last updated:** 2026-06-22T14:06:23-07:00 - **Generated:** 2026-07-08T07:18:31+00:00 ## Executables - stringtie (cli) - stringtie (alias) ## Dependencies - htslib ## Install behavior - Post-install hook: not defined - Bottle: available on arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux ## Freshness - Page generated: 2026-07-08 - Package-manager version: 3.0.3 - Package-manager updated: 2026-06-22 - Local data: ok - Upstream repository: https://github.com/gpertea/stringtie - Upstream latest detected: v3.0.3 (current) ## Project history and usage 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. ### Project history 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. ### Adoption history 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. ### How it is used 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. ### Why package nerds care 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. ### Timeline - 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 ## Security Notes narrow executable package without higher-risk signals. - **Geiger risk:** green / low - narrow executable package without higher-risk signals ## Source Database Details - **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 ## Other Package-Manager Records - 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/ ## Related links - [Source-control packages](https://www.automicvault.com/pkg/source-control-tools/) - Belongs to a source-control command family. - [Terminal utility packages](https://www.automicvault.com/pkg/terminal-utilities/) - Matched terminal and command-line workflow metadata. - [Networking and protocol packages](https://www.automicvault.com/pkg/networking-protocol-tools/) - Matched network, protocol, or remote-service metadata. - [Scientific computing packages](https://www.automicvault.com/pkg/scientific-computing-tools/) - Matched scientific computing metadata. - [htslib](https://www.automicvault.com/pkg/brew/htslib/) - Runtime dependency declared by Homebrew. - [abricate](https://www.automicvault.com/pkg/brew/abricate/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science. - [gffread](https://www.automicvault.com/pkg/brew/gffread/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science. - [minigraph](https://www.automicvault.com/pkg/brew/minigraph/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science. - [tabixpp](https://www.automicvault.com/pkg/brew/tabixpp/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science. - [vcfanno](https://www.automicvault.com/pkg/brew/vcfanno/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science. - [vcflib](https://www.automicvault.com/pkg/brew/vcflib/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science. - [vcftools](https://www.automicvault.com/pkg/brew/vcftools/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science. - [kallisto](https://www.automicvault.com/pkg/brew/kallisto/) - Shares av.db curated category or tags: bioinformatics, cli, quantification, rna-seq, science. - [oarfish](https://www.automicvault.com/pkg/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/automic-vault/db/blob/main/combined/stringtie.yml) ## Sources - Nucleus package database - Geiger risk classifier - package-page enrichment - curated package history - package version freshness - av.db category and tag curation - package relationship graph - external package-manager database matches - cross-ecosystem install command graph