AsaruSim: a single-cell and spatial RNA-Seq Nanopore long-reads simulation workflow.

ABSTRACT:

Motivation

The combination of long-read sequencing technologies like Oxford Nanopore with single-cell RNA sequencing (scRNAseq) assays enables the detailed exploration of transcriptomic complexity, including isoform detection and quantification, by capturing full-length cDNAs. However, challenges remain, including the lack of advanced simulation tools that can effectively mimic the unique complexities of scRNAseq long-read datasets. Such tools are essential for the evaluation and optimization of isoform detection methods dedicated to single-cell long-read studies.

Results

We developed AsaruSim, a workflow that simulates synthetic single-cell long-read Nanopore datasets, closely mimicking real experimental data. AsaruSim employs a multi-step process that includes the creation

SUBMITTER: Hamraoui A 

PROVIDER: S-EPMC11897429 | biostudies-literature | 2025 Mar

REPOSITORIES: biostudies-literature