ArticleGenome biology2021
2passtools: two-pass alignment using machine-learning-filtered splice junctions increases the accuracy of intron detection in long-read RNA sequencing.
Article in Genome biology, 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.
- Review
- Transcriptomics in the era of long-read sequencing.Nature reviews. Genetics · 2025Review
- Discovery of Novel Protein-Coding and Long Non-coding Transcripts in Distinct Regions of the Human Brain.Journal of molecular neuroscience : MN · 2025Article
- Mitochondrial transcriptome of Candida albicans in flagranti - direct RNA sequencing reveals a new layer of information.BMC genomics · 2024Article
- U6 snRNA m6A modification is required for accurate and efficient splicing of C. elegans and human pre-mRNAs.Nucleic acids research · 2024Article
- Long noncoding RNA study: Genome-wide approaches.Genes & diseases · 2023Review
- The Genome-Wide Characterization of Alternative Splicing and RNA Editing in the Development ofJournal of fungi (Basel, Switzerland) · 2023Article
- ESPRESSO: Robust discovery and quantification of transcript isoforms from error-prone long-read RNA-seq data.Science advances · 2023Article
- Excretory/Secretory Proteome of Females and Males of the HookwormPathogens (Basel, Switzerland) · 2023Article
- meLife · 2022Article
- NanoSplicer: accurate identification of splice junctions using Oxford Nanopore sequencing.Bioinformatics (Oxford, England) · 2022Article
- Sequencing of individual barcoded cDNAs using Pacific Biosciences and Oxford Nanopore Technologies reveals platform-specific error patterns.Genome research · 2022Article
- Article
- Quantitative analysis of the splice variants expressed by the major hepatitis B virus genotypes.Microbial genomics · 2021Article
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Authors and funding
4 authors.
Funding
Abstract
Transcription of eukaryotic genomes involves complex alternative processing of RNAs. Sequencing of full-length RNAs using long reads reveals the true complexity of processing. However, the relatively high error rates of long-read sequencing technologies can reduce the accuracy of intron identification. Here we apply alignment metrics and machine-learning-derived sequence information to filter spurious splice junctions from long-read alignments and use the remaining junctions to guide realignment in a two-pass approach. This method, available in the software package 2passtools ( https://github.com/bartongroup/2passtools ), improves the accuracy of spliced alignment and transcriptome assembly for species both with and without existing high-quality annotations.
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