Our most recent blog post, GenArk Hubs Part 4 - New assembly request page describes how to use this new feature.
With the realization that we could not possibly host every single genomic assembly available, we created Assembly Hubs. Assembly Hubs allow anyone to host and view the genome of any species in the context of the UCSC Genome Browser. -Last summer we announced the creation of the Genome Archive +Last summer we announced the creation of the Genome Repository (GenArk) which included Assembly Hubs for the genomic assemblies of more than 1,300 species. Since then, we have taken this a step further by creating this new Assembly Request page that displays about 14,000 assemblies: those that are available for viewing and those that can be requested. We currently have nearly 1,700 assembly hubs available for viewing at the click of a button. Upon first visiting the page shows only the first 500 assemblies. Use the select assembly type to display button to "show all" assemblies. If you don't see the organism or assembly you are interested in then please use the page to request it. We will build an Assembly Hub for you and let you know when it is available for viewing.
We are pleased to announce new GENCODE Gene annotation tracks, which correspond @@ -4892,31 +4892,31 @@
As with many of our assemblies, there are a few different ways to gain access. We have added CHM13 to our Genomes drop-down menu, which provides direct access from almost anywhere on our site. Also, like most of our other genomes, it can be found by searching our Gateway page.
CHM13 is a part of our Genome -Archive (GenArk) system, and thus exists as an system, and thus exists as an assembly hub. GenArk assemblies can always be reached directly via their shortlink URL corresponding to their GCA accession, e.g. CHM13: https://genome.ucsc.edu/h/GCA_009914755.4
Some notable annotations currently available on the CHM13 are listed below. Additional annotations will continue to be added as they become available.
Gene and mRNA annotations:
We would like to thank NCBI and the RefSeq Annotation database for collecting and curating these data. We would also like to thank Hiram Clawson, Lou Nassar, and Gerardo Perez for developing and releasing these tracks.
-Do you have a favorite species or a research organism for which you'd like to visualize the genomic sequence? With the recent addition of genomic assemblies for more than 1,300 species, it's possible that your favorite is now available in the UCSC Genome Browser. Check this list of new assemblies to see if yours is a click away. Each of these Genome Browser assembly hubs comes pre-loaded with several annotation tracks, gene models, and the ability to align genomic sequence to the reference assembly using the BLAT alignment tool. You can add your own data to your view of the assembly hub by uploading a custom track or creating a track hub.
We call this group of assembly hubs, the -Genome Archive (GenArk). The genomes in the GenArk are sourced from +Genome Repository (GenArk). The genomes in the GenArk are sourced from NCBI RefSeq, the Vertebrate Genomes Project (VGP) and other projects. See the complete list of assembly hubs here.
GenArk assemblies can be found by searching the common name (e.g.
American Beaver) or GCA/GCF accession
(e.g. GCF_001984765.1) directly on the
Genome Browser Gateway page.
A full list can also be seen on the GenArk portal which
is organized by phylogenetic groups and projects: