StringTie3 improves total RNA-seq assembly by resolving nascent and mature transcripts.

Co-transcriptional splicing modeling to resolve nascent/mature transcripts + long-read module

StringTie3 is a major update to the StringTie RNA-seq assembler, specifically designed for total rRNA-depleted RNA-seq data. It introduces a nascent mode that separates incomplete co-transcriptional RNA from mature processed isoforms using co-transcriptional splicing modeling, resolving a common source of misassemblies with this strategy. An improved long-read module filters poly(A) priming artifacts from PacBio and ONT data. Across all benchmarked datasets, StringTie3 substantially reduces assembly errors and outperforms existing tools, including on hybrid short+long-read data.

Synthesis written by Geno'X. For the full original abstract, please refer to the source publication.

Total RNA-seq is increasingly used in diagnostics to detect deep splicing variants and aberrant transcripts, with hybrid Illumina + Nanopore strategies emerging in clinical laboratories. StringTie3's ability to distinguish nascent from mature transcripts is crucial to avoid false-positive isoforms in this context. An essential practical update for clinical bioinformatics teams working with diagnostic RNA-seq.

Clinical impact: 1/3 · Evidence strength: 2/3 · Novelty: 2/2 · Sample size: 1/1 · Journal quality: 1/1 → Total: 7/10