install

Additional install commands

macOS

Homebrewverified · 100%

brew install stringtie

local Homebrew formula metadata

Linux

Debian aptverified · 92%

sudo apt install stringtie

Debian stable package indexes · stringtie · source: deb.debian.org

overview

Package summary

Transcript assembly and quantification for RNA-Seq

Project links

Commands and aliases

stringtie

history

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

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

security posture

Risk level: green

narrow executable package without higher-risk signals.

Risk classifier

green risk · low confidence · appliance

Why

narrow executable package without higher-risk signals

Signals

metadata:no-higher-risk-signals

Install behavior

No Homebrew post-install hook is recorded in formula metadata.
Homebrew bottle metadata is available for 6 platform targets.
Installs with 1 runtime dependencies.

Recommended review

Before unattended agent use, check whether the tool reads plaintext credentials, writes remote state, publishes artifacts, or shells out to plugins.

executables

Installed executables

Command	Kind	Exposure	Note
`stringtie`	cli	global executable

freshness

Version and freshness

These signals separate page generation age, package-manager activity, and upstream release comparison. Version lag is warned only when an evidence URL and comparable versions are present.

page generated2026-07-08

manager version3.0.3

manager updated2026-06-22

local dataok

upstreamcurrent

latest detectedv3.0.3

https://github.com/gpertea/stringtie

okNo freshness warnings were generated.

install metadata

Package metadata

Package key	brew:stringtie
Version	3.0.3
Package manager	Homebrew
Package manager page	https://formulae.brew.sh/formula/stringtie
Homepage	https://github.com/gpertea/stringtie
Repository	https://github.com/gpertea/stringtie
Upstream docs	https://ccb.jhu.edu/software/stringtie
License	MIT
Source archive	https://github.com/gpertea/stringtie/archive/refs/tags/v3.0.3.tar.gz
Last updated	2026-06-22T14:06:23-07:00
Pulse	updated
Dependencies	htslib
Bottle	available (on arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux)
Homebrew post-install	not defined
Service	none declared

registry facts

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	https://ghcr.io/v2/homebrew/core
Deprecated	no
Disabled	no
Keg Only	no
URL Keys	head stable

source database matches

Other package-manager records

Matches are pulled from external package-manager indexes and kept separate from local Automic Vault package links.

Debian apt95%

stringtie 2.2.1+ds-3+b1

assemble short RNAseq reads to transcripts

https://ccb.jhu.edu/software/stringtie/

sudo apt install stringtie

Section: science
Architecture: amd64
Source Package: stringtie
5 dependencies
2 optional deps
normalized package name match
Matched by: Stringtie

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

Ubuntu apt95%

stringtie 2.2.1+ds-3build2

assemble short RNAseq reads to transcripts

https://ccb.jhu.edu/software/stringtie/

sudo apt install stringtie

Section: universe/science
Architecture: amd64
5 dependencies
2 optional deps
normalized package name match
Matched by: Stringtie

Ubuntu 24.04 LTS package indexes · archive.ubuntu.com · Ubuntu 24.04 LTS package indexes: stringtie from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz

package graph

Links come from deterministic package relationships, av.db category and tag curation, ecosystem matches, and package hub membership.

source trail

Generated from repository data

This page is generated by av-web from the private package SQLite artifact built by scripts/generate-pkg-sqlite.py.

Combined YAML source

View the package source record on GitHub.

combined/stringtie.yml

Used sources

Geiger risk classifier
Nucleus package database
av.db category and tag curation
cross-ecosystem install command graph
curated package history
external package-manager database matches
package relationship graph
package version freshness
package-page enrichment

Install stringtie with Homebrew, apt