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FUSIM | A software tool for simulating fusion transcripts

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.

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FUSIM forum

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FUSIM classification

FUSIM specifications

Unique identifier:
OMICS_01366
Software type:
Package/Module
Restrictions to use:
None
Input format:
UCSC GenePred table, GFF, GTF, BAM
Output format:
TXT, FASTA
Programming languages:
Java
Computer skills:
Advanced
Stability:
Stable
Name:
FUsion SIMulator
Interface:
Command line interface
Input data:
Number of fusion transcripts to generate, gene model, faidx-indexed reference genome, RNA-seq read alignments
Output data:
Raw fusion sequences
Operating system:
Unix/Linux, Mac OS, Windows
License:
Apache License version 2.0
Version:
0.2.2
Maintained:
Yes

FUSIM distribution

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FUSIM support

Documentation

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Publications

Institution(s)

Department of Biostatistics, SUNY at Buffalo, Buffalo, NY, USA; Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, USA; Center for Computational Research, SUNY at Buffalo, Buffalo, NY, USA

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