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.

Details

Title
GenArk: towards a million UCSC genome browsers
Author
Clawson, Hiram; Lee, Brian T; Raney, Brian J; Barber, Galt P; Casper, Jonathan; Diekhans, Mark; Fischer, Clay; Jairo Navarro Gonzalez; Hinrichs, Angie S; Lee, Christopher M; Nassar, Luis R; Perez, Gerardo; Wick, Brittney; Schmelter, Daniel; Speir, Matthew L; Armstrong, Joel
Pages
1-8
Section
Short Report
Publication year
2023
Publication date
2023
Publisher
BioMed Central
ISSN
14747596
e-ISSN
1474760X
Source type
Scholarly Journal
Language of publication
English
ProQuest document ID
2877498656
Copyright
© 2023. This work is licensed under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.