Supporting data for "Trans-NanoSim characterizes and simulates nanopore RNA-seq data"

Compared to second-generation sequencing technologies, third-generation single-molecule RNA sequencing has unprecedented advantages; the long reads it generates facilitate isoform-level transcript characterization. In particular, the Oxford Nanopore Technology sequencing platforms have become more popular in recent years due to their relatively high affordability and portability compared to other third-generation sequencing technologies. To aid the development of analytical tools that leverage the power of this technology, simulated data provides a cost-effective solution with ground truth. However, nanopore sequence simulator targeting transcriptomic data is not available yet. We introduce Trans-NanoSim, a tool that simulates reads with technical and transcriptome-specific features learnt from nanopore RNA-seq data. We comprehensively benchmarked Trans-NanoSim on direct RNA and cDNA datasets describing human and mouse transcriptomes. Through comparison against other nanopore read simulators, we show the unique advantage and robustness of Trans-NanoSim in capturing the characteristics of nanopore cDNA and direct RNA reads. As a cost-effective alternative to sequencing real transcriptomes, Trans-NanoSim will facilitate the rapid development of analytical tools for nanopore RNA-seq data.