pangenomeswhere

Pangenomeswhere is a term used in genomics to describe a centralized resource or framework for storing and accessing pangenomes—the complete set of genes and sequence content found across the strains, individuals, or populations of a species. The idea is to provide a single referenceable space that supports the integration of multiple genome assemblies and associated annotations, enabling cross-species and cross-population comparisons. It emphasizes distinguishing the core genome, shared by all members, from the accessory genome present only in subsets, as well as structural variants and presence-absence variation.

A key feature of pangenomeswhere is the use of graph-based representations, such as pangenome graphs, to embed sequences from many genomes into a unified coordinate system. This facilitates efficient querying of gene presence, variant paths, and haplotype structures across samples. The data model typically includes standardized metadata, sample provenance, and links to conventional reference genomes, enabling interoperability with existing databases and tools. Access is commonly provided via programmatic APIs and web interfaces for researchers and clinicians.

Potential applications include comparative genomics, population genetics, epidemiology, and crop and livestock breeding, where team-based analyses require consistent and scalable pangenome data. Challenges for realizing a resource like pangenomeswhere include data standardization, interoperability across repositories, privacy considerations for human data, computational scalability, and governance to ensure curation and updates reflect community consensus. See also: pangenome, pan-genomics, pangenome graph, genomic data repositories.