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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...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Cold Spring Harbor Laboratory Press
2020
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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. |
format | Online Article Text |
id | pubmed-7462071 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Cold Spring Harbor Laboratory Press |
record_format | MEDLINE/PubMed |
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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