Tool

SQANTI-SIM

SQANTI-SIM is a simulator of controlled transcript novelty for long-read RNA sequencing (lrRNA-seq) benchmarks. It allows users to manage transcript novelty using popular long-read simulators, simulating realistic scenarios involving unannotated transcripts.

Basic Information

Repository	https://github.com/ConesaLab/SQANTI-SIM
Documentation	https://github.com/ConesaLab/SQANTI-SIM
Main publication (DOI)	10.1186/s13059-023-03127-0 view
Contact email	ana.conesa@csic.es
Authors/Maintainers	Ana Conesa
Type of application	R/python package
Programming languages	Python
Keywords	Omics, Computational Methods, Resources, Transcriptomics, RNA Sequencing (RNA-seq), Data Analysis, Bioinformatics Software and Tools, Analysis packages (R, Python, etc.), Expression Profiling, Computational models and simulations, Biomolecular simulation, Long-read sequencing

Technical details

Input file formats	gff, gtf, fasta
Output file formats	gff, gtf, fasta
Software compatibility	Linux, Mac
Hardware requirements
Type of containerization	None
Wrapper type	None
Compatible tools
Funding resource	EU funding
Funding support	No funding

Statistics

Unique users (last 12 months)	<100
Unique users (since first release)	<100
Software downloads (last 12 months)	<100
Software downloads (since first release)	<100
Jobs submitted (last 12 months)	<100
Jobs submitted (since first release)	<100
Repository clones (last 12 months)	<100
Repository clones (since first release)	<100
Citations (last 12 months)	<100 (~3 as of 15/10/2026)
Citations (since first release)	<100 (12 as of 15/10/2026)
Early-stage researcher effort (development)
Early-stage researcher effort (maintenance)
Technician-supported effort (development)
Technician-supported effort (maintenance)
Other effort (development)
Other effort (maintenance)
Total effort (development)
Total effort (maintenance)

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