ArticleGenome research2020
TransBorrow: genome-guided transcriptome assembly by borrowing assemblies from different assemblers.
Article in Genome research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Vitellogenin receptor mediates heat adaptability of oocyte development in mud crabs and zebrafish.Nature communications · 2025Article
- Transcriptome analysis of two isolates of the tomato pathogen Cladosporium fulvum, uncovers genome-wide patterns of alternative splicing during a host infection cycle.PLoS pathogens · 2024Article
- LAFITE Reveals the Complexity of Transcript Isoforms in Subcellular Fractions.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Article
- Article
- Protocol for transcriptome assembly by the TransBorrow algorithm.Biology methods & protocols · 2023Review
- Improving RNA Assembly via Safety and Completeness in Flow Decompositions.Journal of computational biology : a journal of computational molecular cell biology · 2022Article
- Tiglon enables accurate transcriptome assembly via integrating mappings of different aligners.iScience · 2022Article
- TahcoRoll: fast genomic signature profiling via thinned automaton and rolling hash.Medical review (2021) · 2021Article
- A consensus-based ensemble approach to improve transcriptome assembly.BMC bioinformatics · 2021Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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Registered trials
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