scReadSim 1.4.0

A single-cell RNA-seq and ATAC-seq read simulator.

scReadSim

A single-cell RNA-seq and ATAC-seq read simulator.

Quick Install

Install scReadSim (most updated version) from Github

pip install git+https://github.com/JSB-UCLA/scReadSim.git

or install from PyPI

pip install scReadSim

About

Single-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.

Website

For tutorials and other details, check our website.

License

This pacakge is licensed under the terms of the MIT License.