ArticleGigaScience2020
Trans-NanoSim characterizes and simulates nanopore RNA-sequencing data.
Article in GigaScience, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 34 citations in OpenAlex.
- Review
- The promise of long-read RNA-seq: reducing bias in analyses of allele imbalance.NAR genomics and bioinformatics · 2026Article
- Spatial isoform sequencing at single-cell resolution reveals cell-type-specific spatial isoform variability in multiple brain cell types.Nature methods · 2026Article
- NanoSimFormer: an end-to-end transformer-based nanopore signal simulator with basecaller guidance.Bioinformatics (Oxford, England) · 2026Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Improving gene isoform quantification with miniQuant.Nature biotechnology · 2026Article
- TNRSim - a simulator of truncated oxford nanopore direct RNA long reads for isoform analysis.Frontiers in bioinformatics · 2026Article
- Transcriptomics in the era of long-read sequencing.Nature reviews. Genetics · 2025Review
- Spatial isoform sequencing at sub-micrometer single-cell resolution reveals novel patterns of spatial isoform variability in brain cell types.bioRxiv : the preprint server for biology · 2025Article
- A spatial long-read approach at near-single-cell resolution reveals developmental regulation of splicing and polyadenylation sites in distinct cortical layers and cell types.Nature communications · 2025Article
- Challenges in identifying mRNA transcript starts and ends from long-read sequencing data.Genome research · 2024Review
- Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.Nature methods · 2024Article
- Simulation of nanopore sequencing signal data with tunable parameters.Genome research · 2024Article
- Highly efficient clustering of long-read transcriptomic data with GeLuster.Bioinformatics (Oxford, England) · 2024Article
- TKSM: highly modular, user-customizable, and scalable transcriptomic sequencing long-read simulator.Bioinformatics (Oxford, England) · 2024Article
- SQANTI-SIM: a simulator of controlled transcript novelty for lrRNA-seq benchmark.Genome biology · 2023Article
- SQANTI-SIM: a simulator of controlled transcript novelty for lrRNA-seq benchmark.bioRxiv : the preprint server for biology · 2023Article
- Accurate isoform discovery with IsoQuant using long reads.Nature biotechnology · 2023Article
- Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2.Nature communications · 2023Article
- Characterization and simulation of metagenomic nanopore sequencing data with Meta-NanoSim.GigaScience · 2023Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundCompared with second-generation sequencing technologies, third-generation single-molecule RNA sequencing has unprecedented advantages; the long reads it generates facilitate isoform-level transcript characterization. In particular, the Oxford Nanopore Technology sequencing platforms have become more popular in recent years owing to their relatively high affordability and portability compared with other third-generation sequencing technologies. To aid the development of analytical tools that leverage the power of this technology, simulated data provide a cost-effective solution with ground truth. However, a nanopore sequence simulator targeting transcriptomic data is not available yet.
findingsWe introduce Trans-NanoSim, a tool that simulates reads with technical and transcriptome-specific features learnt from nanopore RNA-sequncing data. We comprehensively benchmarked Trans-NanoSim on direct RNA and complementary DNA datasets describing human and mouse transcriptomes. Through comparison against other nanopore read simulators, we show the unique advantage and robustness of Trans-NanoSim in capturing the characteristics of nanopore complementary DNA and direct RNA reads.
conclusionsAs a cost-effective alternative to sequencing real transcriptomes, Trans-NanoSim will facilitate the rapid development of analytical tools for nanopore RNA-sequencing data. Trans-NanoSim and its pre-trained models are freely accessible at https://github.com/bcgsc/NanoSim.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.