ArticleRNA (New York, N.Y.)2021
FLAME: long-read bioinformatics tool for comprehensive spliceome characterization.
Article in RNA (New York, N.Y.), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Accurate strand-specific long-read transcript isoform discovery and quantification at bulk, single-cell, and single-nucleus resolution.bioRxiv : the preprint server for biology · 2026Article
- Accurate and Cost-Efficient Whole Genome Sequencing of Hepatitis B Virus Using Nanopore.Journal of medical virology · 2025Article
- Quality assessment of long read data in multisample lrRNA-seq experiments using SQANTI-reads.Genome research · 2025Article
- Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation.Genome research · 2025Review
- Review
- Advances in long-read single-cell transcriptomics.Human genetics · 2024Review
- SQANTI-reads: a tool for the quality assessment of long read data in multi-sample lrRNA-seq experiments.bioRxiv : the preprint server for biology · 2024Article
- Nucleotide-level distance metrics to quantify alternative splicing implemented in TranD.Nucleic acids research · 2024Article
- Unraveling the Concealed Transcriptomic Landscape of PTEN in Human Malignancies.Current genomics · 2023Article
- L-GIREMI uncovers RNA editing sites in long-read RNA-seq.Genome biology · 2023Article
- isONform: reference-free transcriptome reconstruction from Oxford Nanopore data.Bioinformatics (Oxford, England) · 2023Article
- Hybrid-seq deciphers the complex transcriptional profile of the humanRNA biology · 2023Article
- L-RAPiT: A Cloud-Based Computing Pipeline for the Analysis of Long-Read RNA Sequencing Data.International journal of molecular sciences · 2022Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Comprehensive characterization of differentially spliced RNA transcripts with nanopore sequencing is limited by bioinformatics tools that are reliant on existing annotations. We have developed FLAME, a bioinformatics pipeline for alternative splicing analysis of gene-specific or transcriptome-wide long-read sequencing data. FLAME is a Python-based tool aimed at providing comprehensible quantification of full-length splice variants, reliable de novo recognition of splice sites and exons, and representation of consecutive exon connectivity in the form of a weighted adjacency matrix. Notably, this workflow circumvents issues related to inadequate reference annotations and allows for incorporation of short-read sequencing data to improve the confidence of nanopore sequencing reads. In this study, the Epstein-Barr virus long noncoding RNA
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