GOPHER

GOPHER (Generator Of Probes for capture Hi-C Experiments at high Resolution) is a versatile Java desktop application specifically developed to facilitate the design of probes for capture Hi-C (CHC) experiments. CHC is a sophisticated technique that combines target enrichment with chromosome conformation-capturing methodologies to investigate the spatial organization of genomic regions at high resolution and cost-effectively. While CHC is commonly used to explore the interactions between regulatory elements and promoters, its utility extends to other genomic investigations.

To accommodate the diverse needs of CHC experiments, GOPHER implements three distinct strategies for CHC probe design:

1. Simple Approach: This method follows the conventional probe design strategy used in many CHC studies, placing one probe at each margin of a single digest overlapping each promoter's transcription start site (TSS).

2. Simple-Patched Approach: This method includes a heuristic to improve the coverage of viewpoints, especially when the TSS is close to one of the digest's boundaries, thereby addressing a common limitation of the simple approach. 3. Extended Approach: Tailored for more focused investigations of smaller gene sets, this strategy allows for a more detailed and specific probe design, potentially encompassing areas beyond promoters, such as GWAS hits or large genomic blocks.

Beyond probe design, GOPHER offers various features to assist users throughout the CHC probe design process. These include the ability to visualize and edit viewpoints, facilitating a more intuitive and user-friendly probe design experience. Additionally, GOPHER generates various output files invaluable for documentation, ordering probes, and conducting downstream analyses.