SQANTI3: curation of long-read transcriptomes for accurate identification of known and novel isoforms

Francisco J Pardo-Palacios; Angeles Arzalluz-Luque; Liudmyla Kondratova; Pedro Salguero; Jorge Mestre-Tomás; Rocío Amorín; Eva Estevan-Morió; Tianyuan Liu; Adalena Nanni; Lauren McIntyre; Elizabeth Tseng; Ana Conesa

doi:10.1038/s41592-024-02229-2

SQANTI3: curation of long-read transcriptomes for accurate identification of known and novel isoforms

Nat Methods. 2024 May;21(5):793-797. doi: 10.1038/s41592-024-02229-2. Epub 2024 Mar 20.

Authors

Francisco J Pardo-Palacios^#^{1

2}, Angeles Arzalluz-Luque^#^{1

2}, Liudmyla Kondratova^{3

4}, Pedro Salguero², Jorge Mestre-Tomás¹, Rocío Amorín^{4

5}, Eva Estevan-Morió¹, Tianyuan Liu¹, Adalena Nanni⁶, Lauren McIntyre^{4

6}, Elizabeth Tseng⁷, Ana Conesa⁸

Affiliations

¹ Institute for Integrative Systems Biology, Spanish National Research Council, Paterna, Valencia, Spain.
² Department of Applied Statistics and Operational Research, and Quality, Universitat Politècnica de València, Valencia, Valencia, Spain.
³ Horticultural Sciences Department, University of Florida, Gainesville, FL, USA.
⁴ Genetics Institute, University of Florida, Gainesville, FL, USA.
⁵ Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA.
⁶ Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA.
⁷ Pacific Biosciences, Menlo Park, CA, USA.
⁸ Institute for Integrative Systems Biology, Spanish National Research Council, Paterna, Valencia, Spain. [email protected].

^# Contributed equally.

Abstract

SQANTI3 is a tool designed for the quality control, curation and annotation of long-read transcript models obtained with third-generation sequencing technologies. Leveraging its annotation framework, SQANTI3 calculates quality descriptors of transcript models, junctions and transcript ends. With this information, potential artifacts can be identified and replaced with reliable sequences. Furthermore, the integrated functional annotation feature enables subsequent functional iso-transcriptomics analyses.

MeSH terms

Gene Expression Profiling / methods
High-Throughput Nucleotide Sequencing / methods
Humans
Molecular Sequence Annotation* / methods
Protein Isoforms / genetics
Sequence Analysis, RNA / methods
Software
Transcriptome*

Grants and funding

R21 HG011280/HG/NHGRI NIH HHS/United States