Related Experiment Video
Updated: May 26, 2025
Sequencing of mRNA from Whole Blood using Nanopore Sequencing
Published on: June 3, 2019
AsaruSim: a single-cell and spatial RNA-Seq Nanopore long-reads simulation workflow
Ali Hamraoui1,2, Laurent Jourdren1, Morgane Thomas-Chollier1,2
1GenomiqueENS, Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris 75005, France.
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 of a synthetic count matrix, generation of perfect reads, optional PCR amplification, introduction of sequencing errors, and comprehensive quality control reporting. Applied to a dataset of human peripheral blood mononuclear cells, AsaruSim accurately reproduced experimental read characteristics.
Availability And Implementation:
The source code and full documentation are available at https://github.com/GenomiqueENS/AsaruSim.
