The UCSC Genome Browser database: 2021 update.

Jairo Navarro Gonzalez ,Daniel Schmelter,Hiram Clawson,David Haussler,Luis R Nassar,Maximilian Haeussler,Mark Diekhans,Conner C Powell,Matthew L Speir,Galt P Barber ,Alastair Charles Fyfe ,Nathan D Maulding ,Jonathan D Casper ,Angie S Hinrichs ,Robert M Kuhn ,Brian J Raney ,Jason D Fernandes ,Christopher M Lee ,Anna Benet‐Pagès ,Ann S Zweig ,Kate R Rosenbloom ,W James Kent

doi:10.1093/nar/gkaa1070

Jairo Navarro Gonzalez , Daniel Schmelter + Show 20 more

Open Access

https://doi.org/10.1093/nar/gkaa1070

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Abstract

For more than two decades, the UCSC Genome Browser database (https://genome.ucsc.edu) has provided high-quality genomics data visualization and genome annotations to the research community. As the field of genomics grows and more data become available, new modes of display are required to accommodate new technologies. New features released this past year include a Hi-C heatmap display, a phased family trio display for VCF files, and various track visualization improvements. Striving to keep data up-to-date, new updates to gene annotations include GENCODE Genes, NCBI RefSeq Genes, and Ensembl Genes. New data tracks added for human and mouse genomes include the ENCODE registry of candidate cis-regulatory elements, promoters from the Eukaryotic Promoter Database, and NCBI RefSeq Select and Matched Annotation from NCBI and EMBL-EBI (MANE). Within weeks of learning about the outbreak of coronavirus, UCSC released a genome browser, with detailed annotation tracks, for the SARS-CoV-2 RNA reference assembly.

Highlights

The UCSC Genome Browser [1] was first released in 2001 as a tool to display the newly assembled human genome
Tool updates are improvements that allow the display of new types of data or permit users to perform new types of analysis
Software updates to the UCSC Genome Browser in previous years have included tools like the Genome Browser in a Box (GBiB) [40] and the Variant Annotation Integrator (VAI) [41]

Summary

Introduction

The UCSC Genome Browser [1] was first released in 2001 as a tool to display the newly assembled human genome. Clicking on a gene in this track allows a user to explore the interaction data for that gene in a new graph visualization tool. Last year seven new hubs were added to this public listing, including three assembly hubs with genomes that are not natively displayed on the Browser.

Results

Conclusion