ArticleBMC bioinformatics2020
Extending rnaSPAdes functionality for hybrid transcriptome assembly.
Article in BMC bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- HyDRA: A pipeline for integrating long- and short-read RNAseq data for custom transcriptome assembly.iScience · 2026Article
- A comprehensive evaluation of long-read de novo transcriptome assembly.Genome biology · 2026Article
- Interpreting fungal ecological contributions through taxonomic and functional profiling of metatranscriptomics.IMA fungus · 2026Review
- How drought and ploidy level shape gene expression and DNA methylation in Phragmites australis.Plant cell reports · 2025Article
- Draft whole genome sequence ofMicrobiology resource announcements · 2025Article
- Influence of developmental stage on the antibiotic resistome and virome of the critically endangered kākāpō (Frontiers in microbiology · 2025Article
- Trans2express - de novo transcriptome assembly pipeline optimized for gene expression analysis.Plant methods · 2024Article
- Identification of novel cattle (Bos taurus) genes and biological insights of their function in pre-implantation embryo development.BMC genomics · 2024Article
- Integrated transcriptomic and WGCNA analyses reveal candidate genes regulating mainly flavonoid biosynthesis in Litsea coreana var. sinensis.BMC plant biology · 2024Article
- Genomic and morphological characterization of a new Thiothrix species from a sulfide hot spring of the Zmeinaya bay (Northern Baikal, Russia).Antonie van Leeuwenhoek · 2024Article
- Enhancing transcriptome analysis in medicinal plants: multiple unigene sets inFrontiers in plant science · 2024Article
- Evaluation of Genetic Diversity and Virulence Potential ofPathogens (Basel, Switzerland) · 2023Article
- Prevalence and Genetic Diversity ofMicroorganisms · 2023Article
- annotate_my_genomes: an easy-to-use pipeline to improve genome annotation and uncover neglected genes by hybrid RNA sequencing.GigaScience · 2022Article
- Structure of a mitochondrial ribosome with fragmented rRNA in complex with membrane-targeting elements.Nature communications · 2022Article
- Improved transcriptome assembly using a hybrid of long and short reads with StringTie.PLoS computational biology · 2022Article
- Resolving the Microalgal Gene Landscape at the Strain Level: a Novel Hybrid Transcriptome ofApplied and environmental microbiology · 2022Article
- Prospects and challenges of cancer systems medicine: from genes to disease networks.Briefings in bioinformatics · 2022Review
- Virulence Determinants and Genetic Diversity ofPathogens (Basel, Switzerland) · 2021Article
- Characterization and Genetic Diversity ofVeterinary sciences · 2021Article
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8 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundDe novo RNA-Seq assembly is a powerful method for analysing transcriptomes when the reference genome is not available or poorly annotated. However, due to the short length of Illumina reads it is usually impossible to reconstruct complete sequences of complex genes and alternative isoforms. Recently emerged possibility to generate long RNA reads, such as PacBio and Oxford Nanopores, may dramatically improve the assembly quality, and thus the consecutive analysis. While reference-based tools for analysing long RNA reads were recently developed, there is no established pipeline for de novo assembly of such data.
resultsIn this work we present a novel method that allows to perform high-quality de novo transcriptome assemblies by combining accuracy and reliability of short reads with exon structure information carried out from long error-prone reads. The algorithm is designed by incorporating existing hybridSPAdes approach into rnaSPAdes pipeline and adapting it for transcriptomic data.
conclusionTo evaluate the benefit of using long RNA reads we selected several datasets containing both Illumina and Iso-seq or Oxford Nanopore Technologies (ONT) reads. Using an existing quality assessment software, we show that hybrid assemblies performed with rnaSPAdes contain more full-length genes and alternative isoforms comparing to the case when only short-read data is used.
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