TransBorrow: genome-guided transcriptome assembly by borrowing assemblies from different assemblers.
KAUST DepartmentComputational Bioscience Research Center (CBRC)
Computer Science Program
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Structural and Functional Bioinformatics Group
Online Publication Date2020-08-17
Print Publication Date2020-08
Permanent link to this recordhttp://hdl.handle.net/10754/664769
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AbstractRNA-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.
CitationYu, T., Mu, Z., Fang, Z., Liu, X., Gao, X., & Liu, J. (2020). TransBorrow: genome-guided transcriptome assembly by borrowing assemblies from different assemblers. Genome Research. doi:10.1101/gr.257766.119
SponsorsThis 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.
PublisherCold Spring Harbor Laboratory
Except where otherwise noted, this item's license is described as This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International).