Transcriptome assembly from long-read RNA-seq alignments with StringTie2

Sam Kovaka, Aleksey V. Zimin, Geo M. Pertea, Roham Razaghi, Steven L. Salzberg, Mihaela Pertea

Research output: Contribution to journalArticlepeer-review

68 Scopus citations


RNA sequencing using the latest single-molecule sequencing instruments produces reads that are thousands of nucleotides long. The ability to assemble these long reads can greatly improve the sensitivity of long-read analyses. Here we present StringTie2, a reference-guided transcriptome assembler that works with both short and long reads. StringTie2 includes new methods to handle the high error rate of long reads and offers the ability to work with full-length super-reads assembled from short reads, which further improves the quality of short-read assemblies. StringTie2 is more accurate and faster and uses less memory than all comparable short-read and long-read analysis tools.

Original languageEnglish (US)
Article number278
JournalGenome biology
Issue number1
StatePublished - Dec 16 2019


  • Gene expression
  • Long-read sequencing
  • RNA-seq
  • Transcriptome assembly

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology


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