SQANTI-SIM: a simulator of controlled transcript novelty for lrRNA-seq benchmark

Long-read RNA sequencing has emerged as a powerful tool for transcript discovery, even in well-annotated organisms. However, assessing the accuracy of different methods in identifying annotated and novel transcripts remains a challenge. Here, we present SQANTI-SIM, a versatile tool that wraps around popular long-read simulators to allow precise management of transcript novelty based on the structural categories defined by SQANTI3. By selectively excluding specific transcripts from the reference dataset, SQANTI-SIM effectively emulates scenarios involving unannotated transcripts. Furthermore, the tool provides customizable features and supports the simulation of additional types of data, representing the first multi-omics simulation tool for the lrRNA-seq field.

Automated summary

SQANTI-SIM is a versatile tool that wraps around popular long-read simulators, allowing precise management of transcript novelty based on the structural categories defined by SQANTI3. It effectively emulates scenarios involving unannotated transcripts and supports the simulation of additional types of data, making it the first multi-omics simulation tool for the lrRNA-seq field.