Skip to content
DraconiticResearch
Search Sources API
188,932 studies31 sourcesUpdated 25 min ago
PreprintCC BYbioRxiv

SQANTI-evidence: isoform-resolved, evidence-tiered structural annotation of unannotated genomes from long-read RNA-seq

  • P. Atienza Lopez1
  • A. Conesa
  1. 1Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia
Read full textPDFDOICite

Abstract

Long-read RNA sequencing captures full-length transcripts, yet current annotation pipelines fail to properly curate the data for gene prediction. We present SQANTI-evidence, a workflow that annotates a genome from long reads alone, without a reference annotation or protein database. SQANTI3-curated transcripts enter the annotation as observed, with isoforms and untranslated regions; AUGUSTUS predicts genes at loci without read support. In benchmarks, the curated layer was the most precise gene set in five of seven species, recovered twice as many exact isoforms as BRAKER in mammals and placed 3' ends nearest the poly(A) site. We annotated 13 ERGA datasets.

Related

  1. Testing immune priming failure in laryngeal squamous cell carcinoma: direct evidence, unresolved links, and a compartment-resolved framework
    Wei-Zhe Hong, Guan-Jiang Huang, Qi-Ping Luo +1
    Frontiers in immunologyPeer-reviewedCC BYFull textImmunologyEurope PMC
  2. Gravlax: an annotation-independent molecular evidence archive for single-cell RNA-seq
    R. Patro
    bioRxivPreprintCC BY-NC-NDFull textBioinformatics & computational biologybioRxiv
  3. Evidence-resolved benchmarks separate biological context recognition from direct-partner specificity in protein interaction models
    H. Cheng, C. Sun, C. Ye +2
    bioRxivPreprintCC BY-NC-NDFull textBioinformatics & computational biologybioRxiv
  4. AFM imaging of milk casein micelles: Evidence for structural rearrangement upon acidification
    Mustapha Ouanezar, Fanny Guyomarc'H, Antoine Bouchoux
    LangmuirPeer-reviewedPublisher termsFull text92 citedGeneral biochemistryGeneral biologyHAL
  5. Long-Read Evidence for Repeat-Associated Structural Heterogeneity in the Mitochondrial Genome of Rhododendron spinuliferum
    Jie Chen, Yikai Feng, Xinyi Qian +1
    GenesPeer-reviewedCC BYFull textGenetics & genomicsEurope PMC

Cite

BibTeXRIS
BibTeX
@misc{lopez2026sqantievidence,
  title = {{SQANTI-evidence: isoform-resolved, evidence-tiered structural annotation of unannotated genomes from long-read RNA-seq}},
  author = {P. Atienza Lopez and A. Conesa},
  howpublished = {bioRxiv},
  year = {2026},
  month = nov,
  doi = {10.64898/2026.11.01.763455},
  url = {https://www.biorxiv.org/content/10.64898/2026.11.01.763455v1},
  note = {CC BY},
}
RIS
TY  - UNPB
TI  - SQANTI-evidence: isoform-resolved, evidence-tiered structural annotation of unannotated genomes from long-read RNA-seq
AU  - P. Atienza Lopez
AU  - A. Conesa
PY  - 2026
DA  - 2026/11/01
PB  - bioRxiv
DO  - 10.64898/2026.11.01.763455
UR  - https://www.biorxiv.org/content/10.64898/2026.11.01.763455v1
AB  - Long-read RNA sequencing captures full-length transcripts, yet current annotation pipelines fail to properly curate the data for gene prediction. We present SQANTI-evidence, a workflow that annotates a genome from long reads alone, without a reference annotation or protein database. SQANTI3-curated transcripts enter the annotation as observed, with isoforms and untranslated regions; AUGUSTUS predicts genes at loci without read support. In benchmarks, the curated layer was the most precise gene set in five of seven species, recovered twice as many exact isoforms as BRAKER in mammals and placed 3' ends nearest the poly(A) site. We annotated 13 ERGA datasets.
ER  -