GOPHER is a Java App designed to help design probes for Capture Hi-C experiments. GOPHER allows users to download, uncompress, and index genome FASTA files, which are used to calculate the size and repeat content of restriction fragments within candidate viewpoints. A list of candidate genes is uploaded to the App, and the app calculates viewpoints and allows users to revise them using an interactive visualization.

Please download the app from the Releases page. You will require Java 17 or higher to run Gopher. On most computers you should be able to start the app with a double click. (Note to M1/M2 MacIntosh users - we have noted that problems occur with JavaFX applications such as GOPHER on M1 Macs with Java 17; we recommend using the Java 19 JDK from Azul Zulu). If desired, you can also start Gopher from the command line as follows.

java -jar GOPHER-0.9.0.jar

We recommend starting GOPHER with 2Gb (min)/6Gb (max) memory.

java -Xms2g -Xmx6g -jar GOPHER-0.9.0.jar

GOPHER will run without problems on 2GB for small panels (-Xmx2g), but 6GB is preferable for probe design for all protein-coding genes or other very larger panels.

The manual for GOPHER can be found here: https://thejacksonlaboratory.github.io/Gopher

See Hansen P, et al., 2019, GOPHER: Generator Of Probes for capture Hi-C Experiments at high Resolution. BMC Genomics 20:40 for more information.