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. 2023 Jan 6;51(D1):D1188-D1195.
doi: 10.1093/nar/gkac1072.

The UCSC Genome Browser database: 2023 update

Luis R Nassar  1 , Galt P Barber  1 , Anna Benet-Pagès  2   3 , Jonathan Casper  1 , Hiram Clawson  1 , Mark Diekhans  1 , Clay Fischer  1 , Jairo Navarro Gonzalez  1 , Angie S Hinrichs  1 , Brian T Lee  1 , Christopher M Lee  1 , Pranav Muthuraman  1 , Beagan Nguy  1 , Tiana Pereira  1 , Parisa Nejad  1 , Gerardo Perez  1 , Brian J Raney  1 , Daniel Schmelter  1 , Matthew L Speir  1 , Brittney D Wick  1 , Ann S Zweig  1 , David Haussler  1 , Robert M Kuhn  1 , Maximilian Haeussler  1 , W James Kent  1
Affiliations

The UCSC Genome Browser database: 2023 update

Luis R Nassar et al. Nucleic Acids Res. .

Abstract

The UCSC Genome Browser (https://genome.ucsc.edu) is an omics data consolidator, graphical viewer, and general bioinformatics resource that continues to serve the community as it enters its 23rd year. This year has seen an emphasis in clinical data, with new tracks and an expanded Recommended Track Sets feature on hg38 as well as the addition of a single cell track group. SARS-CoV-2 continues to remain a focus, with regular annotation updates to the browser and continued curation of our phylogenetic sequence placing tool, hgPhyloPlace, whose tree has now reached over 12M sequences. Our GenArk resource has also grown, offering over 2500 hubs and a system for users to request any absent assemblies. We have expanded our bigBarChart display type and created new ways to visualize data via bigRmsk and dynseq display. Displaying custom annotations is now easier due to our chromAlias system which eliminates the requirement for renaming sequence names to the UCSC standard. Users involved in data generation may also be interested in our new tools and trackDb settings which facilitate the creation and display of their custom annotations.

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Figures

Figure 1.
Figure 1.
Recommended Track Sets available for hg38 in the Genome Browser menu (Genome Browser → Recommended Track Sets).
Figure 2.
Figure 2.
Single-cell RNA-seq track group now available on hg38.
Figure 3.
Figure 3.
Advanced options in Track Search now includes the option to search Public Hub tracks.
Figure 4.
Figure 4.
Search facets for bigBarChart track Tabula Sapiens: Tabula Tissue Cell.
Figure 5.
Figure 5.
(A) Full display mode in bigRmsk track. (B) dynseq display in full mode.
See this image and copyright information in PMC

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