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

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Type
Article
Authors
Yu, Ting
Mu, Zengchao
Fang, Zhaoyuan
Liu, Xiaoping
Gao, Xin cc
Liu, Juntao
KAUST Department
Computational Bioscience Research Center (CBRC)
Computer Science Program
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Structural and Functional Bioinformatics Group
KAUST Grant Number
BAS/1/1624
FCC/1/1976-18-01
FCC/1/1976-23-01
FCC/1/1976-25-01
FCC/1/1976-26-01
Date
2020-08-17
Online Publication Date
2020-08-17
Print Publication Date
2020-08
Submitted Date
2019-07-30
Permanent link to this record
http://hdl.handle.net/10754/664769

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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.
Citation
Yu, 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
Sponsors
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.
Publisher
Cold Spring Harbor Laboratory
Journal
Genome research
DOI
10.1101/gr.257766.119
PubMed ID
32817072
Additional Links
http://genome.cshlp.org/lookup/doi/10.1101/gr.257766.119
Collections
Articles; Structural and Functional Bioinformatics Group; Computer Science Program; Computational Bioscience Research Center (CBRC); Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International).
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).