stringtie ☆
« Back to VersTracker
Description:
Transcript assembly and quantification for RNA-Seq
Type: Formula  |  Tracked Since: Dec 28, 2025
Links: Homepage  |  formulae.brew.sh
Category: Other
Tags: bioinformatics rna-seq transcriptomics genomics assembly
Install: brew install stringtie
About:
StringTie is a fast and highly efficient assembler for RNA-Seq read assemblies. It constructs transcripts by assembling aligned reads using a novel network flow algorithm, followed by a clustering step that merges overlapping transcripts. It also provides quantitative estimates of transcript abundance, making it a comprehensive solution for transcriptome reconstruction and expression analysis.
Key Features:
  • Efficient network flow algorithm for transcript assembly
  • Built-in quantification of transcript abundance (FPKM/TPM)
  • Support for guided assembly using reference annotations
  • Handles novel transcripts and alternative splicing events
Use Cases:
  • De novo transcriptome assembly from RNA-Seq data
  • Quantifying gene and transcript expression levels
  • Identifying novel transcripts and fusion genes
Alternatives:
  • Cufflinks – Cufflinks is an older alternative; StringTie is generally faster and more memory-efficient.
  • Trinity – Trinity is designed for deep de novo assembly but is significantly more resource-intensive than StringTie.
Version History
Detected Version Rev Change Commit
Sep 16, 2025 3:34am 0 VERSION_BUMP 201fc4b4
« Back to VersTracker  |  Browse Packages  |  About