The UCSC Genome Browser

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ABSTRACT The UCSC Genome Browser and associated tools are used by hundreds of thousands of biomedical researchers including clinical geneticists, bioinformaticians, researchers working with model organisms, and wet lab scientists researching human physiology at the molecular level in both healthy and disease states. The browser integrates the results of thousands of biomedical labs – including a wide range of biochemical assays, genetic studies, curations, sequencing projects, and computer analyses into a series of tracks aligned to the underlying genomic sequence. The genome provides a natural integration framework for these diverse data sources, which the browser showcases at a variety of display scales ranging from the single base to individual genes, entire chromosomes, and ultimately to the genome as a whole. The Genome Browser is implemented using robust, fast, high-quality software capable of handling over one million hits per day. This web software provides a window into an exceptionally detailed and well-documented database that can be queried computationally as well as browsed graphically. The database is loaded with a suite of programs, developed both at UCSC and elsewhere, capable of distilling huge genomics data sets into high-quality annotations of the genome. Significant engineering effort is invested to ensure the quality of the software and data sets, including those developed by external contributors. The system is designed to make it easy for users to view their own, unpublished, data sets alongside those that we have fully curated and integrated. Consortia and other resources can make their data visible in our browser via “track hubs.” We plan to extend our resource in significant ways. We will help make genomics more equitable to currently underserved populations by moving to a more inclusive “pangenome” reference that includes sequences that represent the greater genomic diversity of humanity, not just samples of convenience from largely European populations. We will enable visualization of individual genomes, not just a single haploid reference genome. We will address the opportunities and challenges of new technologies such as single-cell RNA sequencing and single-molecule long-read DNA sequencing. We will collaborate with others in the increasingly complex ecosystem of biomedical consortia and resources, and will integrate their results into the Genome Browser, and also, through our APIs and our helpful staff, ensure that others can make the best use of data available in their efforts. We will provide tools and data for medical users to understand the significance of sequence variants in the patients they care for and will help characterize regions of greater genomic complexity and medical importance. We will extend our outreach effort to include more online content to help engage a new generation of users.