SQANTI3
Tool for the quality control of long-reads transcript models
Basic Information
| Repository | https://github.com/ConesaLab/SQANTI3 |
| Documentation | https://github.com/ConesaLab/SQANTI3/wiki |
| Main publication (DOI) | 10.1038/s41592-024-02229-2 view |
| Contact email | ana.conesa@csic.es |
| Authors/Maintainers | Carlos Blanco Gómez, Fabián Robledo Yagüe, Ana Conesa, Pablo Atienza López |
| Type of application | R/python package |
| Programming languages | PythonRBASH / Shell |
| Keywords | Omics, Computational Methods, Resources, Transcriptomics, RNA Sequencing (RNA-seq), Data Analysis, Artificial Intelligence, Machine Learning in Biology, Bioinformatics Software and Tools, Annotation tools, Analysis packages (R, Python, etc.), Data Visualization, Applications of Computational Biology, Model organisms, Bioinformatics enabling techniques, Standards in Computational Biology, Benchmarking, Long-read sequencing |
Technical details
| Input file formats | tsv, bam, gtf, bed, fasta, json |
| Output file formats | tsv, bam, gtf, fasta, html, pdf |
| Software compatibility | Linux, Mac |
| Hardware requirements | At least 8 GB RAM |
| Type of containerization | Conda |
| Wrapper type | None |
| Compatible tools | FLAIR; IsoAnnot; Every tool producing a GTF: IsoQuant, Bambu, FLAIR, IsoCall; IsoSeq3; TALON; tappAS; Kallisto |
| Funding resource | EU funding, National competitive funding |
| Funding support | No funding |
Statistics
| Unique users (last 12 months) | 100-1000 |
| Unique users (since first release) | 100-1000 |
| Software downloads (last 12 months) | 100-1000 |
| Software downloads (since first release) | 100-1000 |
| Jobs submitted (last 12 months) | |
| Jobs submitted (since first release) | |
| Repository clones (last 12 months) | |
| Repository clones (since first release) | |
| Citations (last 12 months) | <100 (~95 as of 15/10/2026) |
| Citations (since first release) | 100-1000 (203 as of 15/10/2026) |
| Early-stage researcher effort (development) | 1-2 |
| Early-stage researcher effort (maintenance) | 0-1 |
| Technician-supported effort (development) | |
| Technician-supported effort (maintenance) | |
| Other effort (development) | |
| Other effort (maintenance) | |
| Total effort (development) | |
| Total effort (maintenance) |