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

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 assembl...

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Detalles Bibliográficos
Autores principales: Yu, Ting, Mu, Zengchao, Fang, Zhaoyuan, Liu, Xiaoping, Gao, Xin, Liu, Juntao
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7462071/
https://www.ncbi.nlm.nih.gov/pubmed/32817072
http://dx.doi.org/10.1101/gr.257766.119
Descripción
Sumario: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.