A single-cell RNA-seq and ATAC-seq read simulator.
For more details about scReadSim, you can check out our manuscript on Nature Communications:
Yan, G., Song, D., & Li, J. J. (2023). scReadSim: a single-cell RNA-seq and ATAC-seq read simulator. Nature Communications, 14(1), 7482. https://doi.org/10.1038/s41467-023-43162-w
Install scReadSim (most updated version) from Github
pip install git+https://github.com/JSB-UCLA/scReadSim.gitor install from PyPI
pip install scReadSimSingle-cell sequencing technologies emerged and diversified rapidly in the past few years, along with the successful development of many computational tools. Realistic simulators can help researchers benchmark computational tools. However, few simulators can generate single-cell multi-omics data, and none can generate reads directly. To fill in this gap, we propose scReadSim, a simulator for single-cell multi-omics reads. Trained on real data, scReadSim generates synthetic sequencing reads in BAM or FASTQ formats. We deployed scReadSim on a sci-ATAC-seq dataset and a single-cell multimodal dataset to show the resemblance between synthetic data and real data at the read and count levels. Moreover, we show that scReadSim allows user-specified ground truths of accessible chromatin regions for single-cell chromatin accessibility data generation. In addition, scReadSim is flexible for allowing varying throughputs and library sizes as input parameters to guide experimental design.
For tutorials and other details, check our website.
Any questions or suggestions on scReadSim are welcomed! Please report it on issues, or contact Guanao Yan ([email protected]).
- scDesign2: Sun, T., Song, D., Li, W. V., & Li, J. J. (2021). scDesign2: a transparent simulator that generates high-fidelity single-cell gene expression count data with gene correlations captured. Genome biology, 22(1), 1-37.
- scDesign3: Song, D., Wang, Q., Yan, G., Liu, T., Sun, T., & Li, J. J. (2024). scDesign3 generates realistic in silico data for multimodal single-cell and spatial omics. Nature Biotechnology, 42(2), 247-252.
This pacakge is licensed under the terms of the MIT License.