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.
Please refer to Wiki for how to install and use SQANTI-SIM:
SQANTI-SIM supports running multiple simulation jobs in parallel. To avoid potential race conditions when multiple jobs access the same genome file simultaneously, pre-create the genome index file before launching parallel jobs:
# Pre-create the .fai index file
samtools faidx genome.fa
# Example: Run parallel jobs with different simulators or parameters
# Job 1: PBSIM3 simulation
python sqanti-sim.py sim --pbsim \
--genome genome.fa \
--gtf annotation.gtf \
--trans_index index.tsv \
--dir output_pbsim \
--cores 1 &
# Job 2: NanoSim ONT simulation
python sqanti-sim.py sim --ont \
--genome genome.fa \
--gtf annotation.gtf \
--trans_index index.tsv \
--dir output_ont \
--read_type cDNA &
# Job 3: Different expression profile
python sqanti-sim.py sim --pbsim \
--genome genome.fa \
--gtf annotation.gtf \
--trans_index index_high_expression.tsv \
--dir output_high_expr \
--cores 1 &
wait # Wait for all jobs to completeThis ensures that all temporary files are properly isolated in job-specific directories and prevents file collisions between parallel jobs.
Current version (25/09/2025): 0.3.1
Updates, patches and releases:
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