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FUSIM / FUsion SIMulator

Simulates fusion transcripts. The simulation of events known to create fusion genes and their resulting chimeric proteins is supported, including inter-chromosome translocation, trans-splicing, complex chromosomal rearrangements, and transcriptional read through events. FUSIM provides the ability to assemble a dataset of fusion transcripts useful for testing and benchmarking applications in fusion gene discovery, and enables comprehensive testing in silico of fusion discovery methods in transcriptome sequencing data.

RSS / RNA Seq Simulator

Simulates over dispersed, multiple replica, differential, non-stranded RNA-Seq datasets. RNA Seq Simulator takes SAM alignment files from RNA-Seq data. This method can generate in silico reads. It requires real RNA-seq data as input, and then simulates various types of factors that cause differential gene expression. This tool is part of USeq, a collection of software tools for both low and high level analysis of next generation sequencing (NGS), ultra high throughput signature sequencing data from the Solexa, SOLiD, and 454 platforms.

RNASeqReadSimulator

Generates simulated single-end or paired-end RNA-Seq reads. RNASeqReadSimulator is a set of scripts that provides users an application to allow experienced users to expand functions. It allows users to randomly assign expression levels of transcripts and generate simulated single-end or paired-end RNA-Seq reads. It is also able to simulate random read errors from sequencing platforms. All scripts are command line driven and allows users to invoke and design more functions.