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

Ting Yu | Zendy; Zengchao Mu | Zendy; Zhaoyuan Fang | Zendy; Xiaoping Liu | Zendy; Xin Gao | Zendy; Juntao Liu | Zendy

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

Author(s) -

Ting Yu,

Zengchao Mu,

Zhaoyuan Fang,

Xiaoping Liu,

Xin Gao,

Juntao Liu

Publication year - 2020

Publication title -

genome research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.556

H-Index - 297

eISSN - 1549-5469

pISSN - 1088-9051

DOI - 10.1101/gr.257766.119

Subject(s) - biology , transcriptome , de novo transcriptome assembly , computational biology , rna seq , rna splicing , sequence assembly , path (computing) , genome , alternative splicing , gene , rna , genetics , exon , computer science , gene expression , programming language

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.

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