Welcome to FuSpot

FuSpot is a local alignment and visualization tool that, simply, puts the power to evaluate real-world gene fusions in your hands. Using a novel alignment technique, FuSpot will simultaneously align reads to fusion and non-fusion gene transcripts. This, in tandem with FuSpot's read extraction tool, builds a comprehensive picture of your candidate fusion breakpoint by visualizing the alignments of all the reads local to your breakpoint. Download the read extraction tool, use it to retrieve reads local to your breakpoint, then upload them here after entering the candidate fusion breakpoint coordinates to get started.

Align and Visualize

Breakpoint Coordinates:

References: Auto Custom

Enter the genomic coordinates of a fusion breakpoint and FuSpot will retrieve the genomic sequences as well as the sequences of the nearest exons of both fusion gene partners to use for alignment:

Genome Build:

5' End



Reference Length:

Gene Name:

3' End



Reference Length:

Gene Name:


Alignment Type:

Generate Example Breakpoint

*All file sizes must be less than 4Mb.

Single-End Reads:

Read File*

Paired-End Reads:

First Mate File*
Second Mate File*

Align and Visualize


Visualize Saved Alignment

Enter an XML file previously downloaded from FuSpot:

XML File

Multiple Runs?

How to get reads to input to FuSpot?

Align with a Chimeric-capable RNA aligner. Then download our read extraction tool and run it on your aligned file to get reads local to the candidate fusion.

Download Extraction Tool