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The UCSC Genome Browser database: 2026 update

Jonathan D. Casper, Matthew L Speir, Brian J. Raney, Gerardo Perez, Luis R Nassar, Christopher M. Lee et al. · 2025 · 141 citationsRead the paper

Now in its 25th year of operation, the UCSC Genome Browser (https://genome.ucsc.edu) provides a central location for researchers around the world to display and compare annotations on assembled genomes. Highlighted updates include a positional heatmap display, used to show data on functional consequences of mutation from MaveDB; QuickLift, a tool to copy annotation data seen on one assembly for display on another related assembly; and HubSpace, an initiative to simplify the process of creating and using track hubs by providing each user account with dedicated storage on UCSC's infrastructure.

What the full text shows

Deployed in practice
  • Implementation of QuickLift for dynamic annotation transposition between genome assemblies. (Requires a liftOver alignment between source and destination assemblies)
  • Provision of dedicated storage for user track and assembly hubs via HubSpace. — 10–20 GB per account (UCSC infrastructure)
  • Integration of MaveDB multiplexed assays of variant effects (MAVEs) using a positional heatmap display. (Point mutations in functional elements)
  • Updated ClinVar track display using colored diamonds to mark protein-truncating mutations. (GRCh37/hg19 and GRCh38/hg38 assemblies; affects splice acceptor, splice donor, frameshift, and nonsense variants)
  • Support for bedMethyl data files for epigenetic state visualization. (Nanopore sequencing assays)
  • Expansion of the GenArk project to provide basic browsers for a vast number of genome assemblies. — Over 28,000 genome assemblies (RefSeq and GenBank data)
Setup
Web-based platform serving thousands of users daily, primarily focused on GRCh37/hg19 and GRCh38/hg38 human assemblies.
How
The paper describes software updates and feature implementations for a web-based genomic visualization platform. It details the integration of new data formats (bedMethyl), display styles (heatmaps, decorators), and data migration tools (QuickLift).
Limitations
QuickLift requires pre-existing liftOver alignments. · Current user data tools require transmission to UCSC servers, potentially violating HIPAA/legal requirements for restricted data.

Summarized by Gemma 4 from the open-access full text · 10 Oct 2026. Read it