Dataset Information

GenArk: towards a million UCSC genome browsers.

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.

SUBMITTER: Clawson H

PROVIDER: S-EPMC10544498 | biostudies-literature | 2023 Oct

REPOSITORIES: biostudies-literature

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GenArk: towards a million UCSC genome browsers.

Clawson Hiram H Lee Brian T BT Raney Brian J BJ Barber Galt P GP Casper Jonathan J Diekhans Mark M Fischer Clay C Gonzalez Jairo Navarro JN Hinrichs Angie S AS Lee Christopher M CM Nassar Luis R LR Perez Gerardo G Wick Brittney B Schmelter Daniel D Speir Matthew L ML Armstrong Joel J Zweig Ann S AS Kuhn Robert M RM Kirilenko Bogdan M BM Hiller Michael M Haussler David D Kent W James WJ Haeussler Maximilian M

Genome biology 20231002 1

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 w ...[more]

PMID: 37784172

Dataset Information

GenArk: towards a million UCSC genome browsers.

Publications

GenArk: towards a million UCSC genome browsers.

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