ArticlePLoS computational biology2022
Improved transcriptome assembly using a hybrid of long and short reads with StringTie.
Article in PLoS computational biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 303 papers.
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303 citing papers in PubMed.
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- A gap-free, telomere-to-telomere chromosome-scale genome assembly of the mangrove red snapper, Lutjanus argentimaculatus.Scientific data · 2026Article
- A pangenome of tetraploid wheat reveals the genetic architecture underlying domestication and genomic diversity for breeding.Nature genetics · 2026Article
- Long-read RNA-seq maps the isoform landscape of the trigeminal ganglion in an allergic rhinitis mouse model.BMC genomics · 2026Article
- The Nigella damascena genome provides insights into transposable element-driven genomic gigantism and trait evolution.Nature communications · 2026Article
- Blind genomic tree scans identify loci underlying adaptive peaks in Antirrhinum.bioRxiv : the preprint server for biology · 2026Article
- SpliSync: Genomic language model-driven splice site correction of long RNA sequencing reads.bioRxiv : the preprint server for biology · 2026Article
- The Trichinella Super-Pangenome Reveals the Evolution of Encapsulation and Predicted Host-Parasite Protein Interactions.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
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243 more citing papers are in PubMed but not listed here.
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4 authors.
Funding
Abstract
Short-read RNA sequencing and long-read RNA sequencing each have their strengths and weaknesses for transcriptome assembly. While short reads are highly accurate, they are rarely able to span multiple exons. Long-read technology can capture full-length transcripts, but its relatively high error rate often leads to mis-identified splice sites. Here we present a new release of StringTie that performs hybrid-read assembly. By taking advantage of the strengths of both long and short reads, hybrid-read assembly with StringTie is more accurate than long-read only or short-read only assembly, and on some datasets it can more than double the number of correctly assembled transcripts, while obtaining substantially higher precision than the long-read data assembly alone. Here we demonstrate the improved accuracy on simulated data and real data from Arabidopsis thaliana, Mus musculus, and human. We also show that hybrid-read assembly is more accurate than correcting long reads prior to assembly while also being substantially faster. StringTie is freely available as open source software at https://github.com/gpertea/stringtie.
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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.