SPARK: in silico simulations for benchmarking nascent RNA sequencing experiments

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.

• Publication year

  2025

• Venue

  bioRxiv

• Publication date

  2025-11-08

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1101/2025.11.06.687082PMID 41279502PMCID 12637524
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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