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

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Tác giả: Ali Hamraoui, Laurent Jourdren, Morgane Thomas-Chollier

Ngôn ngữ: eng

Ký hiệu phân loại: 809.008 History and description with respect to kinds of persons

Thông tin xuất bản: England : Bioinformatics (Oxford, England) , 2025

Mô tả vật lý:

Bộ sưu tập: NCBI

ID: 691433

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.
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