ArticleGenome biology2023
SQANTI-SIM: a simulator of controlled transcript novelty for lrRNA-seq benchmark.
Article in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 11 citations in OpenAlex.
- Bramble: projection of spliced genomic alignments into transcriptomic space for improved transcript quantification.bioRxiv : the preprint server for biology · 2026Article
- TUSCO: benchmarking transcriptome reconstruction with endogenous single-isoform controls.Nature communications · 2026Article
- A comprehensive evaluation of long-read de novo transcriptome assembly.Genome biology · 2026Article
- Systematic evaluation of long- and short-read RNA-seq for human peripheral blood.NAR molecular medicine · 2026Article
- Full-length transcriptome ofPlant biotechnology (Tokyo, Japan) · 2025Article
- Transcriptomics in the era of long-read sequencing.Nature reviews. Genetics · 2025Review
- Long-read RNA sequencing unveils a novel cryptic exon in MNAT1 along with its full-length transcript structure in TDP-43 proteinopathy.Communications biology · 2025Article
- Challenges in identifying mRNA transcript starts and ends from long-read sequencing data.Genome research · 2024Review
- Article
- 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
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Long-read RNA sequencing has emerged as a powerful tool for transcript discovery, even in well-annotated organisms. However, assessing the accuracy of different methods in identifying annotated and novel transcripts remains a challenge. Here, we present SQANTI-SIM, a versatile tool that wraps around popular long-read simulators to allow precise management of transcript novelty based on the structural categories defined by SQANTI3. By selectively excluding specific transcripts from the reference dataset, SQANTI-SIM effectively emulates scenarios involving unannotated transcripts. Furthermore, the tool provides customizable features and supports the simulation of additional types of data, representing the first multi-omics simulation tool for the lrRNA-seq field.
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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.