SQANTI3 is the newest version of the SQANTI tool (publication) that merges features from SQANTI, (code repository) and SQANTI2 (code repository), 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, that also includes IsoAnnot and tappAS.

Current version (10/05/2021): SQANTI3 version 4.2

New features implemented in SQANTI3

version 4.2:

• Extra aligner for mapping Long-Read sequences: uLTRA . To use it, set the option --aligner_choice uLTRA.
• NMD prediction now takes into account the 50bp rule, meaning that isoforms will be tagged as TRUE for prediction_NMD if there's a predicted ORF and CDS ends at least 50bp before the last junction.
• Fixed minor bugs

version 4.1:

• Change for --gtf argument. Now, by default, SQANTI3 will expect a GTF file as input. It will still be possible to provide the sequences of your isoforms as a FASTA or FASTQ file by activatingt the --fasta option.
• New plots and minor bugs of the report fixed.

version 4.0:

• Creation of HTML report. Using the --report argument, it is possible to choose which type of report: html (default), pdf, both or skip.
• Short-reads processing pipeline included. Now, providing directly your short-read data (FASTA/FASTQ format), SQANTI3 will:
  • Map them against the genome to identify SJ and calculate their coverage.
  • Calculate the "ratio_TSS" value for each isoform of your transcriptome.
  • If pair-end data is provided, isoform expression will be computed using kallisto.
• New subcategories for FSM: Reference match, Alternative 3' UTR, Alternative 5' UTR and Alternative 5' and 3' UTRs.
• IsoAnnotLite implemented to generate tappAS compatible GFF3 files. GFF3 output may incorporate functional annotation labels for model species supported by tappAS.
• New plots:
  • Saturation curves only plot when --saturation option activated.
• Installation provided as a conda yml environment file

Please, visit our wiki for more detailed information

• What is SQANTI3?
• SQANTI3 dependencies and installation
• Running SQANTI3 Quality Control
• Running SQANTI3 rules filter
• SQANTI3 output explanation

SQANTI3 paper is in preparation, in the meantime it is possible to cite the original SQANTI paper.

Tardaguila M, de la Fuente L, Marti C, et al. 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. doi:10.1101/gr.222976.117