scReadSim: a single-cell RNA-seq and ATAC-seq read simulator

scReadSim is a single-cell RNA-seq and ATAC-seq read simulator. It starts from the BAM file of the input sequencing data and generates the synthetic dataset using BAM or FASTQ formats. The synthetic data generated by scReadSim resembles the real data in both the count and read level.

Workflow of scReadSim for generating scATAC-seq reads

Workflow of scReadSim for generating scRNA-seq reads

Installation

Install the latest version from GitHub,

run:

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

or:

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

Or quick install from PyPI:

pip install scReadSim

Overview

Tutorials