GenArk: towards a million UCSC genome browsers.
Journal
Genome biology
ISSN: 1474-760X
Titre abrégé: Genome Biol
Pays: England
ID NLM: 100960660
Informations de publication
Date de publication:
02 10 2023
02 10 2023
Historique:
received:
15
03
2023
accepted:
11
09
2023
medline:
4
10
2023
pubmed:
3
10
2023
entrez:
2
10
2023
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 37784172
doi: 10.1186/s13059-023-03057-x
pii: 10.1186/s13059-023-03057-x
pmc: PMC10544498
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
217Subventions
Organisme : NIAID NIH HHS
ID : 75N93019C00076
Pays : United States
Organisme : NHGRI NIH HHS
ID : U41 HG007234
Pays : United States
Organisme : NHGRI NIH HHS
ID : U41HG007234
Pays : United States
Organisme : NHGRI NIH HHS
ID : U24-HG00237
Pays : United States
Commentaires et corrections
Type : UpdateOf
Informations de copyright
© 2023. BioMed Central Ltd., part of Springer Nature.
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