SQANTI3 is the newest version of the SQANTI tool that merges features from SQANTI and SQANTI2, together with new additions. SQANTI3 will continue as an integrated development aiming to provide the best characterization for your new long read-defined transcriptome.
SQANTI3 is the first module of the Functional IsoTranscriptomics (FIT) framework, which also includes IsoAnnot and tappAS.
The latest SQANTI3 release (04/12/2024) is version 5.3.0. See our wiki for installation instructions.
For informacion about previous releases and features introduced in them, see the version history.
WARNING: v5.0 represented a major release of the SQANTI3 software. Versions of SQANTI3 >= 5.0 will not have backward compatibility with previous releases and their output (v4.3 and earlier). Users that wish to apply any of the new functionalities in v5.0 to output files from older versions will herefore need to re-run SQANTI3 QC. See below for a full list of changes implemented in SQANTI3 v5.0.
For detailed documentation, please visit the SQANTI3 wiki.
Please, note that we are currently updating and expanding the wiki to provide as much information as possible and enhance the SQANTI3 user experience. Pages under construction -or where information is still missing- will be indicated where appropriate. Thank you for your patience!
If you are using SQANTI3 in your research, please cite the following paper in addition to this repository:
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Pardo-Palacios, F.J., Arzalluz-Luque, A. et al. SQANTI3: curation of long-read transcriptomes for accurate identification of known and novel isoforms. Nat Methods (2024). https://doi.org/10.1038/s41592-024-02229-2
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Keil, N., Monzó, C., McIntyre, L., Conesa, A. SQANTI-reads: a tool for the quality assessment of long read data in multi-sample lrRNA-seq experiments. BioRxiv (2024) https://www.biorxiv.org/content/10.1101/2024.08.23.609463v2