TransBorrow: genome-guided transcriptome assembly by borrowing assemblies from different assemblers.

Ting Yu, Zengchao Mu, Zhaoyuan Fang, Xiaoping Liu, Xin Gao, Juntao Liu

Research output: Contribution to journalArticlepeer-review

14 Scopus citations

Abstract

RNA-seq technology is widely used in various transcriptomic studies and provides great opportunities to reveal the complex structures of transcriptomes. To effectively analyze RNA-seq data, we introduce a novel transcriptome assembler, TransBorrow, which borrows the assemblies from different assemblers to search for reliable subsequences by building a colored graph from those borrowed assemblies. Then, by seeding reliable subsequences, a newly designed path extension strategy accurately searches for a transcript-representing path cover over each splicing graph. TransBorrow was tested on both simulated and real data sets and showed great superiority over all the compared leading assemblers.
Original languageEnglish (US)
JournalGenome research
DOIs
StatePublished - Aug 21 2020

Bibliographical note

KAUST Repository Item: Exported on 2020-10-01
Acknowledged KAUST grant number(s): BAS/1/1624, FCC/1/1976-18-01, FCC/1/1976-23-01, FCC/1/1976-25-01, FCC/1/1976-26-01
Acknowledgements: This work was supported by the National Natural Science Foundation of China with code 61801265, and King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR) under award numbers BAS/1/1624-01, FCC/1/1976-18-01, FCC/1/1976-23-01, FCC/1/1976-25-01, FCC/1/1976-26-01, REI/1/0018-01-01, REI/1/4216-01-01, and URF/1/4098-01-01. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Fingerprint

Dive into the research topics of 'TransBorrow: genome-guided transcriptome assembly by borrowing assemblies from different assemblers.'. Together they form a unique fingerprint.

Cite this