smartSim

smartSim simulates Smart-seq3 single-cell RNA sequencing reads to generate realistic data that reflects the complexities of single-cell transcriptomics for benchmarking computational tools.

Key Features:

• Splicing event simulation: smartSim simulates known and novel splicing events.
• Read type generation: smartSim generates both UMI-containing and internal reads.
• Protocol-specific bias modeling: smartSim mimics protocol-specific biases by leveraging empirical data distributions.
• Realistic data properties: smartSim-generated data closely resembles real Smart-seq3 datasets in terms of fragment length distributions, internal read counts, and read quality scores.
• Output format: smartSim generates raw sequencing reads in FASTQ format, making it compatible with both genome- and transcriptome-based alignment tools.

Scientific Applications:

• Benchmarking isoform reconstruction: smartSim provides data for evaluating computational tools for isoform reconstruction in single-cell RNA sequencing.
• Benchmarking splicing quantification: smartSim enables assessment of computational methods for splicing quantification.
• Alternative splicing detection evaluation: smartSim supports evaluation of computational methods for alternative splicing detection in single-cell RNA sequencing.

Methodology:

smartSim leverages empirical data distributions to mimic protocol-specific biases and generates raw sequencing reads in FASTQ format.