GenArk: Towards a Million UCSC Genome Browsers

Overview

Journal Genome Biol

Specialties Biology
Genetics

Date 2023 Oct 2

PMID 37784172

Authors

Hiram Clawson

Brian T Lee

Brian J Raney

Galt P Barber

Jonathan Casper

Mark Diekhans

Clay Fischer

Jairo Navarro Gonzalez

Angie S Hinrichs

Christopher M Lee

Luis R Nassar

Gerardo Perez

Brittney Wick

Daniel Schmelter

Matthew L Speir

Joel Armstrong

Ann S Zweig

Robert M Kuhn

Bogdan M Kirilenko

Michael Hiller

David Haussler

W James Kent

Maximilian Haeussler

Affiliations

Soon will be listed here.

Abstract

Interactive graphical genome browsers are essential tools in genomics, but they do not contain all the recent genome assemblies. We create Genome Archive (GenArk) collection of UCSC Genome Browsers from NCBI assemblies. Built on our established track hub system, this enables fast visualization of annotations. Assemblies come with gene models, repeat masks, BLAT, and in silico PCR. Users can add annotations via track hubs and custom tracks. We can bulk-import third-party resources, demonstrated with TOGA and Ensembl gene models for hundreds of assemblies.Three thousand two hundred sixty-nine GenArk assemblies are listed at https://hgdownload.soe.ucsc.edu/hubs/ and can be searched for on the Genome Browser gateway page.

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