StringTie

A tool to assemble RNA-seq sequence alignments into transcripts. The StringTie algorithm can optionally make de novo assemblies and uses a novel network flow algorithm.

Topic

Transcriptomics;RNA-seq

Detail

  • Operation: Transcriptome assembly;RNA-Seq analysis

  • Software interface: Command-line user interface

  • Language: C++;C

  • License: The MIT License

  • Cost: Free

  • Version name: -

  • Credit: The US National Institutes of Health (NIH), the Cancer Prevention and Research Institute of Texas

  • Input: BAM

  • Output: -

  • Contact: mpertea@jhu.edu

  • Collection: -

  • Maturity: Stable

Publications

  • StringTie enables improved reconstruction of a transcriptome from RNA-seq reads.
  • Pertea M, et al. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. 2015; 33:290-5. doi: 10.1038/nbt.3122
  • https://doi.org/10.1038/nbt.3122
  • PMID: 25690850
  • PMC: PMC4643835
  • Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown.
  • Pertea M, et al. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. 2016; 11:1650-67. doi: 10.1038/nprot.2016.095
  • https://doi.org/10.1038/nprot.2016.095
  • PMID: 27560171
  • PMC: PMC5032908

Download and documentation

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