Precise Transcript Reconstruction with End-Guided Assembly

ABSTRACT Accurate annotation of transcript isoforms is crucial to understand gene functions, but automated methods for reconstructing full-length transcripts from RNA sequencing (RNA-seq) data remain imprecise. We developed Bookend, a software package for transcript assembly that incorporates data from different RNA-seq techniques, with a focus on identifying and utilizing RNA 5′ and 3′ ends. Through end-guided assembly with Bookend we demonstrate that correct modeling of transcript start and end sites is essential for precise transcript assembly. Furthermore, we discovered that utilization of end-labeled reads present in full-length single-cell RNA-seq (scRNA-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, as well as meta-assembly of RNA-seq from single mouse embryonic stem cells (mESCs) can produce end-to-end transcript annotations of comparable quality to reference annotations in these model organisms. Summary statement Bookend is a generalized framework that utilizes RNA 5′ and 3′ end information hidden in RNA-seq datasets to accurately reconstruct transcriptomes including those from single cells.