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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
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author Yu, Ting
Mu, Zengchao
Fang, Zhaoyuan
Liu, Xiaoping
Gao, Xin
Liu, Juntao
author_facet Yu, Ting
Mu, Zengchao
Fang, Zhaoyuan
Liu, Xiaoping
Gao, Xin
Liu, Juntao
author_sort Yu, Ting
collection PubMed
description 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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spelling pubmed-74620712020-09-11 TransBorrow: genome-guided transcriptome assembly by borrowing assemblies from different assemblers Yu, Ting Mu, Zengchao Fang, Zhaoyuan Liu, Xiaoping Gao, Xin Liu, Juntao Genome Res Method 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. Cold Spring Harbor Laboratory Press 2020-08 /pmc/articles/PMC7462071/ /pubmed/32817072 http://dx.doi.org/10.1101/gr.257766.119 Text en © 2020 Yu et al.; Published by Cold Spring Harbor Laboratory Press http://creativecommons.org/licenses/by/4.0/ This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
spellingShingle Method
Yu, Ting
Mu, Zengchao
Fang, Zhaoyuan
Liu, Xiaoping
Gao, Xin
Liu, Juntao
TransBorrow: genome-guided transcriptome assembly by borrowing assemblies from different assemblers
title TransBorrow: genome-guided transcriptome assembly by borrowing assemblies from different assemblers
title_full TransBorrow: genome-guided transcriptome assembly by borrowing assemblies from different assemblers
title_fullStr TransBorrow: genome-guided transcriptome assembly by borrowing assemblies from different assemblers
title_full_unstemmed TransBorrow: genome-guided transcriptome assembly by borrowing assemblies from different assemblers
title_short TransBorrow: genome-guided transcriptome assembly by borrowing assemblies from different assemblers
title_sort transborrow: genome-guided transcriptome assembly by borrowing assemblies from different assemblers
topic Method
url 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
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