Bookend precise transcript reconstruction with end-guided assembly

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.

Bibliographic Details

Main Authors:	Schon, Michael A., Lutzmayer, Stefan, Hofmann, Falko, Nodine, Michael D.
Format:	Article/Letter to editor biblioteca
Language:	English
Subjects:	5′ and 3′ ends, Capping, Iso-Seq, Long-read, PAS, Polyadenylation, RNA-seq, Single-cell, TSS, Transcriptome,
Online Access:	https://research.wur.nl/en/publications/bookend-precise-transcript-reconstruction-with-end-guided-assembl
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