ArticleGenome biology2022
RATTLE: reference-free reconstruction and quantification of transcriptomes from Nanopore sequencing.
Article in Genome biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
- Review
- Beyond the gene: isoform diversity as a key contributor to human brain disorders.Current opinion in genetics & development · 2026Review
- Fungen: clustering and correcting long-read metatranscriptomic data for exploring eukaryotic microorganisms.Science China. Life sciences · 2026Article
- Transcriptome Profiling of Leaves and Roots from Rooibos (Plants (Basel, Switzerland) · 2026Article
- Improving gene isoform quantification with miniQuant.Nature biotechnology · 2026Article
- A comprehensive evaluation of long-read de novo transcriptome assembly.Genome biology · 2026Article
- Long-Read Sequencing Reveals RNA Splicing Complexity in Human Diseases.Computational and structural biotechnology journal · 2026Review
- Transcriptomics in the era of long-read sequencing.Nature reviews. Genetics · 2025Review
- Spider venom peptides with unique fold selectively block Shaker-type potassium channels.Cellular and molecular life sciences : CMLS · 2025Article
- Transcriptome dataset of leaves treated with different spectra of light-emitting diodes onData in brief · 2025Article
- De novo clustering of large long-read transcriptome datasets with isONclust3.Bioinformatics (Oxford, England) · 2025Article
- Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation.Genome research · 2025Review
- cONcat: Computational reconstruction of concatenated fragments from long Oxford Nanopore reads.PloS one · 2025Article
- TDFPS-Designer: an efficient toolkit for barcode design and selection in nanopore sequencing.Genome biology · 2024Article
- Mitochondrial transcriptome of Candida albicans in flagranti - direct RNA sequencing reveals a new layer of information.BMC genomics · 2024Article
- Biochemical-free enrichment or depletion of RNA classes in real-time during direct RNA sequencing with RISER.Nature communications · 2024Article
- Coordinated wound responses in a regenerative animal-algal holobiont.Nature communications · 2024Article
- Transcriptome dataset of gall-rust infected Sengon (Data in brief · 2024Article
- Highly efficient clustering of long-read transcriptomic data with GeLuster.Bioinformatics (Oxford, England) · 2024Article
- Article
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8 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Nanopore sequencing enables the efficient and unbiased measurement of transcriptomes. Current methods for transcript identification and quantification rely on mapping reads to a reference genome, which precludes the study of species with a partial or missing reference or the identification of disease-specific transcripts not readily identifiable from a reference. We present RATTLE, a tool to perform reference-free reconstruction and quantification of transcripts using only Nanopore reads. Using simulated data and experimental data from isoform spike-ins, human tissues, and cell lines, we show that RATTLE accurately determines transcript sequences and their abundances, and shows good scalability with the number of transcripts.
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