GenArk: towards a million UCSC genome browsers

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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 an...

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Detalles Bibliográficos
Autores principales: Clawson, Hiram, Lee, Brian T., Raney, Brian J., Barber, Galt P., Casper, Jonathan, Diekhans, Mark, Fischer, Clay, Gonzalez, Jairo Navarro, Hinrichs, Angie S., Lee, Christopher M., Nassar, Luis R., Perez, Gerardo, Wick, Brittney, Schmelter, Daniel, Speir, Matthew L., Armstrong, Joel, Zweig, Ann S., Kuhn, Robert M., Kirilenko, Bogdan M., Hiller, Michael, Haussler, David, Kent, W. James, Haeussler, Maximilian
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Short Report
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10544498/
https://www.ncbi.nlm.nih.gov/pubmed/37784172
http://dx.doi.org/10.1186/s13059-023-03057-x
Descripción
Sumario: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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-023-03057-x.

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