SPARK: in silico simulations for benchmarking nascent RNA sequencing experiments

Calvo-Roitberg, E.; Lehman, J. W.; Tam, E.; Elhajjajy, S.; Engelhardt, B. E.; Pai, A. A.

doi:10.1101/2025.11.06.687082

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bioRxiv · 10.1101/2025.11.06.687082

SPARK: in silico simulations for benchmarking nascent RNA sequencing experiments

Calvo-Roitberg, E.·Lehman, J. W.·Tam, E.·Elhajjajy, S.·Engelhardt, B. E.·Pai, A. A.

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Abstract

Nascent RNA sequencing offers profound insights into transcriptional dynamics, yet there are substantial challenges to analyzing these data. The development of proper computational tools necessitates realistic benchmarking datasets that reflect biological variability and technical biases. We present simulated pre-mRNA and RNA kinetics (SPARK), a versatile in silico framework for generating reads across nascent RNA sequencing approaches. SPARK simulates the process of transcription -- allowing for variable elongation rates and pausing events -- and key experimental features. SPARK provides a comprehensive platform for computational development and benchmarking in nascent RNA genomics.

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Calvo-Roitberg, E., Lehman, J. W., Tam, E., Elhajjajy, S., Engelhardt, B. E., Pai, A. A.. 2025-11-08. SPARK: in silico simulations for benchmarking nascent RNA sequencing experiments. https://doi.org/10.1101/2025.11.06.687082

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