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

Autor: Pardo-Palacios FJ; Institute for Integrative Systems Biology, Spanish National Research Council, Paterna, Valencia, Spain.; Department of Applied Statistics and Operational Research, and Quality, Universitat Politècnica de València, Valencia, Valencia, Spain., Arzalluz-Luque A; Institute for Integrative Systems Biology, Spanish National Research Council, Paterna, Valencia, Spain.; Department of Applied Statistics and Operational Research, and Quality, Universitat Politècnica de València, Valencia, Valencia, Spain., Kondratova L; Horticultural Sciences Department, University of Florida, Gainesville, FL, USA.; Genetics Institute, University of Florida, Gainesville, FL, USA., Salguero P; Department of Applied Statistics and Operational Research, and Quality, Universitat Politècnica de València, Valencia, Valencia, Spain., Mestre-Tomás J; Institute for Integrative Systems Biology, Spanish National Research Council, Paterna, Valencia, Spain., Amorín R; Genetics Institute, University of Florida, Gainesville, FL, USA.; Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA., Estevan-Morió E; Institute for Integrative Systems Biology, Spanish National Research Council, Paterna, Valencia, Spain., Liu T; Institute for Integrative Systems Biology, Spanish National Research Council, Paterna, Valencia, Spain., Nanni A; Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA., McIntyre L; Genetics Institute, University of Florida, Gainesville, FL, USA.; Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA., Tseng E; Pacific Biosciences, Menlo Park, CA, USA., Conesa A; Institute for Integrative Systems Biology, Spanish National Research Council, Paterna, Valencia, Spain. ana.conesa@csic.es.
Jazyk: angličtina
Zdroj: Nature methods [Nat Methods] 2024 May; Vol. 21 (5), pp. 793-797. Date of Electronic Publication: 2024 Mar 20.
DOI: 10.1038/s41592-024-02229-2
Abstrakt: 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.
(© 2024. The Author(s).)
Databáze: MEDLINE
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