Bookend precise transcript reconstruction with end-guided assembly

Michael A. Schon*, Stefan Lutzmayer, Falko Hofmann, Michael D. Nodine

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

4 Citations (Scopus)


We developed Bookend, a package for transcript assembly that incorporates data from different RNA-seq techniques, with a focus on identifying and utilizing RNA 5′ and 3′ ends. We demonstrate that correct identification of transcript start and end sites is essential for precise full-length transcript assembly. Utilization of end-labeled reads present in full-length single-cell RNA-seq datasets dramatically improves the precision of transcript assembly in single cells. Finally, we show that hybrid assembly across short-read, long-read, and end-capture RNA-seq datasets from Arabidopsis thaliana, as well as meta-assembly of RNA-seq from single mouse embryonic stem cells, can produce reference-quality end-to-end transcript annotations.

Original languageEnglish
Article number143
JournalGenome Biology
Publication statusPublished - Dec 2022


  • 5′ and 3′ ends
  • Capping
  • Iso-Seq
  • Long-read
  • PAS
  • Polyadenylation
  • RNA-seq
  • Single-cell
  • Transcriptome
  • TSS


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