Genome Biology (Oct 2023)

GenArk: towards a million UCSC genome browsers

  • 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

DOI
https://doi.org/10.1186/s13059-023-03057-x
Journal volume & issue
Vol. 24, no. 1
pp. 1 – 8

Abstract

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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.