RNA-Seq Read Simulator

RNA-Seq is now a common protocol to study the expression of genes or transcripts. For research purposes, there are many simulators to simulate RNA-Seq reads, like Flux Simulator. But many times I found it hard to use because: 1) there are complicated parameters, 2) it requires large memory and 3) it crushes frequently. So I wrote a few scripts to generate simulated RNA-Seq reads, and publish them in a package "RNASeqReadSimulator".

 RNASeqReadSimulator is a set of scripts generating simulated RNA-Seq reads. It provides users a simple tool to generate RNA-Seq reads for research purposes, and a framework to allow experienced users to expand functions. RNASeqReadSimulator offers the following features:

1. It allows users to randomly assign expression levels of transcripts and generate simulated single-end or paired-end RNA-Seq reads. 
2. It is able to generate RNA-Seq reads that have a specified positional bias profile. 
3. It is able to simulate random read errors from sequencing platforms. 
4. The simulator consists of a few simple Python scripts. All scripts are command line driven, allowing users to invoke and design more functions.

The webpage of RNASeqReadSimulator is here. You can find the source code in GitHub.