SQANTI3: Curation of Long-read Transcriptomes for Accurate Identification of Known and Novel Isoforms

Overview

Journal Nat Methods

Specialties Biomedical Engineering
Pathology

Date 2024 Mar 21

PMID 38509328

Authors

Francisco J Pardo-Palacios

Angeles Arzalluz-Luque

Liudmyla Kondratova

Pedro Salguero

Jorge Mestre-Tomas

Rocio Amorin

Eva Estevan-Morio

Tianyuan Liu

Adalena Nanni

Lauren McIntyre

Elizabeth Tseng

Ana Conesa

Affiliations

Soon will be listed here.

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.

Citing Articles

A systematic benchmark of Nanopore long-read RNA sequencing for transcript-level analysis in human cell lines.

Chen Y, Davidson N, Kei Wan Y, Yao F, Su Y, Gamaarachchi H Nat Methods. 2025; .

PMID: 40082608 DOI: 10.1038/s41592-025-02623-4.

A cell-type specific surveillance complex represses cryptic promoters during differentiation in an adult stem cell lineage.

Matias N, Gallicchio L, Lu D, Kim J, Perez J, Detweiler A bioRxiv. 2025; .

PMID: 40060570 PMC: 11888433. DOI: 10.1101/2025.02.25.640250.

Discovery of Novel Protein-Coding and Long Non-coding Transcripts in Distinct Regions of the Human Brain.

Santucci K, Cheng Y, Xu S, Gao Y, Lindner G, Takenaka K J Mol Neurosci. 2025; 75(1):30.

PMID: 40048072 PMC: 11885362. DOI: 10.1007/s12031-025-02316-9.

Transcriptomic Analysis Reveals Patterns of Expression of Stage-Specific Genes in Early Embryos.

Su R, Chen Y, Zhu R, Ding G, Dong K, Feng M Genes (Basel). 2025; 16(2).

PMID: 40004516 PMC: 11855871. DOI: 10.3390/genes16020187.

Heterozygosity at a conserved candidate sex determination locus is associated with female development in the clonal raider ant.

Lacy K, Lee J, Rozen-Gagnon K, Wang W, Carroll T, Kronauer D bioRxiv. 2025; .

PMID: 39975376 PMC: 11838215. DOI: 10.1101/2025.01.24.634795.

References

Dong X, Du M, Gouil Q, Tian L, Jabbari J, Bowden R . Benchmarking long-read RNA-sequencing analysis tools using in silico mixtures. Nat Methods. 2023; 20(11):1810-1821. DOI: 10.1038/s41592-023-02026-3. View

Garalde D, Snell E, Jachimowicz D, Sipos B, Lloyd J, Bruce M . Highly parallel direct RNA sequencing on an array of nanopores. Nat Methods. 2018; 15(3):201-206. DOI: 10.1038/nmeth.4577. View

Abugessaisa I, Noguchi S, Hasegawa A, Kondo A, Kawaji H, Carninci P . refTSS: A Reference Data Set for Human and Mouse Transcription Start Sites. J Mol Biol. 2019; 431(13):2407-2422. DOI: 10.1016/j.jmb.2019.04.045. View

Tian L, Jabbari J, Thijssen R, Gouil Q, Amarasinghe S, Voogd O . Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing. Genome Biol. 2021; 22(1):310. PMC: 8582192. DOI: 10.1186/s13059-021-02525-6. View

Takahashi H, Lassmann T, Murata M, Carninci P . 5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing. Nat Protoc. 2012; 7(3):542-61. PMC: 4094379. DOI: 10.1038/nprot.2012.005. View

Herrmann C, Schmidt R, Kanitz A, Artimo P, Gruber A, Zavolan M . PolyASite 2.0: a consolidated atlas of polyadenylation sites from 3' end sequencing. Nucleic Acids Res. 2019; 48(D1):D174-D179. PMC: 7145510. DOI: 10.1093/nar/gkz918. View

Pardo-Palacios F, Wang D, Reese F, Diekhans M, Carbonell-Sala S, Williams B . Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. Nat Methods. 2024; 21(7):1349-1363. PMC: 11543605. DOI: 10.1038/s41592-024-02298-3. View

Weirather J, de Cesare M, Wang Y, Piazza P, Sebastiano V, Wang X . Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis. F1000Res. 2017; 6:100. PMC: 5553090. DOI: 10.12688/f1000research.10571.2. View

Li H . Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018; 34(18):3094-3100. PMC: 6137996. DOI: 10.1093/bioinformatics/bty191. View

10.

Soneson C, Yao Y, Bratus-Neuenschwander A, Patrignani A, Robinson M, Hussain S . A comprehensive examination of Nanopore native RNA sequencing for characterization of complex transcriptomes. Nat Commun. 2019; 10(1):3359. PMC: 6668388. DOI: 10.1038/s41467-019-11272-z. View

11.

Bray N, Pimentel H, Melsted P, Pachter L . Near-optimal probabilistic RNA-seq quantification. Nat Biotechnol. 2016; 34(5):525-7. DOI: 10.1038/nbt.3519. View

12.

Beaudoing E, Freier S, Wyatt J, Claverie J, Gautheret D . Patterns of variant polyadenylation signal usage in human genes. Genome Res. 2000; 10(7):1001-10. PMC: 310884. DOI: 10.1101/gr.10.7.1001. View

13.

Singh M, Al-Eryani G, Carswell S, Ferguson J, Blackburn J, Barton K . High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes. Nat Commun. 2019; 10(1):3120. PMC: 6635368. DOI: 10.1038/s41467-019-11049-4. View

14.

Tardaguila M, de la Fuente L, Marti C, Pereira C, Pardo-Palacios F, Del Risco H . SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification. Genome Res. 2018; 28(3):396-411. PMC: 5848618. DOI: 10.1101/gr.222976.117. View

15.

Lucas M, Novoa E . Long-read sequencing in the era of epigenomics and epitranscriptomics. Nat Methods. 2023; 20(1):25-29. DOI: 10.1038/s41592-022-01724-8. View

16.

Rodriguez J, Pozo F, Cerdan-Velez D, Di Domenico T, Vazquez J, Tress M . APPRIS: selecting functionally important isoforms. Nucleic Acids Res. 2021; 50(D1):D54-D59. PMC: 8728124. DOI: 10.1093/nar/gkab1058. View

17.

Marx V . Method of the year: long-read sequencing. Nat Methods. 2023; 20(1):6-11. DOI: 10.1038/s41592-022-01730-w. View

18.

Foord C, Hsu J, Jarroux J, Hu W, Belchikov N, Pollard S . The variables on RNA molecules: concert or cacophony? Answers in long-read sequencing. Nat Methods. 2023; 20(1):20-24. DOI: 10.1038/s41592-022-01715-9. View

19.

Volden R, Palmer T, Byrne A, Cole C, Schmitz R, Green R . Improving nanopore read accuracy with the R2C2 method enables the sequencing of highly multiplexed full-length single-cell cDNA. Proc Natl Acad Sci U S A. 2018; 115(39):9726-9731. PMC: 6166824. DOI: 10.1073/pnas.1806447115. View

20.

Veeneman B, Shukla S, Dhanasekaran S, Chinnaiyan A, Nesvizhskii A . Two-pass alignment improves novel splice junction quantification. Bioinformatics. 2015; 32(1):43-9. PMC: 5006238. DOI: 10.1093/bioinformatics/btv642. View