Installation · Documentation · Report bug · SQANTI3

SQANTI-SIM is an open-source long-read RNA-seq (LRS) simulation tool designed to generate high-fidelity ONT and PacBio transcriptome long reads with precise control over transcript novelty based on SQANTI3 structural categories, along with orthogonal data supporting both known and novel transcripts.

By building upon the capabilities of NanoSim, PBSIM3, and IsoSeqSim to simulate long reads using the provided GTF, SQANTI-SIM generates both simulated reads and a reduced GTF with excluded transcripts flagged as novel. Additionally, SQANTI-SIM goes a step further by generating matching Illumina and CAGE data for the simulated LRS, thus faithfully reproducing LRS transcriptome datasets.

Documentation

Please refer to Wiki for how to install and use SQANTI-SIM:

• Overview

• Requirements and installation

• Parameters summary

• Run SQANTI-SIM

• SQANTI-SIM: classif

• SQANTI-SIM: design

• SQANTI-SIM: sim

• Tutorial

Change Log

Current version (11/02/2024): 0.2.2

Updates, patches and releases:

• Change log

How to cite SQANTI-SIM

Please cite the following publication if you're using SQANTI-SIM in your research:

• Mestre-Tomás, J., Liu, T., Pardo-Palacios, F., & Conesa, A. (2023). SQANTI-SIM: a simulator of controlled transcript novelty for lrRNA-seq benchmark. Genome Biology, 24(1), 286. https://doi.org/10.1186/s13059-023-03127-0