SQANTI3

Tool for the quality control of long-reads transcript models

Info

Members (researchers): Ana Conesa, Carlos Blanco Gómez, Fabián Robledo Yagüe

Research Groups: Genomics of Gene Expression

Contact Email: ana.conesa@csic.es

Tool Repository: https://github.com/ConesaLab/SQANTI3

Documentation: https://github.com/ConesaLab/SQANTI3/wiki

Publications DOI: 10.1038/s41592-024-02229-2; 10.1101/2023.08.23.554392.

Institution: Instituto de Biología Integrativa de Sistemas (I2SYSBIO)

Application domain:

Analysis packages (R, Python, etc.), Annotation tools, Applications of Computational Biology, Artificial Intelligence, Benchmarking, Bioinformatics enabling techniques, Bioinformatics Software and Tools, Data Analysis, Data Visualization, Machine Learning in Biology, Model organisms, RNA Sequencing (RNA-seq), Standards in Computational Biology, Transcriptomics

Technical details
Type of application
  • R/python package
Software compatibility
  • Linux
  • Mac
Hardware requirements
  • At least 8 GB RAM
Programming language
  • BASH
  • Python
  • R
Type of containerization
  • Conda
Wrapper type
  • None
Input file formats
  • bam
  • bed
  • fasta
  • gtf
  • json
  • tsv
Output file formats
  • bam
  • fasta
  • gtf
  • html
  • pdf
  • tsv
Compatibility with other tools
  • FLAIR
  • IsoAnnot
  • IsoQuant. Every tool producing a GTF
  • Isoseq3
  • TALON
  • tappAS