NDLI: Bookend: precise transcript reconstruction with end-guided assembly

Content Provider	Springer Nature : BioMed Central
Author	Schon, Michael A. Lutzmayer, Stefan Hofmann, Falko Nodine, Michael D.
Abstract	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.
Related Links	https://genomebiology.biomedcentral.com/counter/pdf/10.1186/s13059-022-02700-3.pdf
Ending Page	21
Page Count	21
Starting Page	1
File Format	HTM / HTML
DOI	10.1186/s13059-022-02700-3
Journal	Genome Biology
Issue Number	1
Volume Number	23
Language	English
Publisher	BioMed Central
Publisher Date	2022-06-29
Access Restriction	Open
Subject Keyword	Animal Genetics and Genomics Human Genetics Plant Genetics and Genomics Microbial Genetics and Genomics Bioinformatics Evolutionary Biology RNA-seq Transcriptome Single-cell TSS PAS Capping Polyadenylation 5′ and 3′ ends Long-read Iso-Seq
Content Type	Text
Resource Type	Article
Subject	Biotechnology Genetics
Journal Impact Factor	10.1/2023
5-Year Journal Impact Factor	16.5/2023

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3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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Bookend: precise transcript reconstruction with end-guided assembly

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Publisher Correction: Bookend: precise transcript reconstruction with end-guided assembly

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Bookend: precise transcript reconstruction with end-guided assembly