Last year we announced the creation of a new collection of GenArk assembly hubs. GenArk hubs are constructed from NCBI Genbank GCA/GCF accessioned assembly data, for instance where GCF_001984765.1 is the accession for an American beaver assembly. When present in UCSC’s GenArk collection, these genome browsers can be loaded instantly with direct links (e.g., http://genome.ucsc.edu/h/GCF_001984765.1), and they come ready with dynamically invoked BLAT and PCR servers, enabling searching for sequences and primers. The first released GenArk hubs were organized into phylogenetic groups, for example, all bird assemblies were listed here.
Our newly added genome assembly request page displays which assemblies are available for viewing, and presents a single-click “request” button to send an email to UCSC to add any GCA/GCF assembly available at NCBI not yet part of the GenArk collection.
GenArk currently has over 1,700 assembly hubs available for browsing at the click of a “view” button. To view only those in the current collection, you can use the middle “select assembly type to display” option and remove the “Request browser” checkbox, and only completed browsers will show. Upon first visiting the page shows only the first 500 assemblies. Use the “select assembly type to display” to “show all” assemblies if you do not see your assembly. Click “view” to launch a specific genome browser listed on the page. This earliest version of the page has some performance issues, and selections may take some time, a future improvement planned is to present an active wait cursor when the page is busy filtering results.
By using the “choose clade to view/hide” option it is possible to subselect groups, such as only displaying plants, when narrowing down which genomes may exist or could be requested.
The first “show/hide columns” option on the page enables displaying additional metadata, such as adding the assembly build date or Biosample number, where links exist back to NCBI for more information.
If NCBI does not have a GCA/GCF accession for your desired assembly then our scripts will not be able to pull the data and generate the GenArk addition. Such new assemblies will need to be submitted to NCBI first, after which you can then notify UCSC. You can find directions at NCBI for how to submit new genomes: https://www.ncbi.nlm.nih.gov/assembly/docs/submission/ Also, please review the UCSC GenArk Blog posts for more information on accessing and using tools on GenArk hubs.
If after reading this blog post you have any public questions, please email genome@soe.ucsc.edu. All messages sent to that address are archived on a publicly accessible forum. If your question includes sensitive data, you may send it instead to genome-www@soe.ucsc.edu.
This blog post is the final of three to discuss the Genome Archive (GenArk) assembly hubs. This third post discusses the technical infrastructure of the GenArk hubs, while the first post was about accessing the data, and the second shared examples of using the data.
TECHNICAL DETAILS
What are the systems behind GenArk hubs?
In essence, GenArk hubs are assembly hubs that have been added as Public Hubs.
Anyone can build Track Hubs and Assembly Hubs, where finished hubs can then be requested to be published as Public Hubs. UCSC does have a Public Hub Guidelines page to encourage hub developers to document their data fully before submitting for inclusion, this is mainly to ensure users of Public Hubs know who to contact for their data and can understand what they are visualizing.
To aid independent groups that do not want to build assembly hubs, when the underlying assembly data is already available at NCBI, our engineers have crafted scripts to build these files automatically. GenArk scripts pull data from NCBI and then programmatically construct all of the binary-indexed files needed to visualize them on the UCSC Genome Browser. Additional special features have been included, especially the ability to generate and provide BLAT and PCR dynamic servers through the pre-generation of special index files. Our engineers have also optimized other elements of these GenArk Hubs by applying the latest available Track Hub features.
But what are the internal methods UCSC uses to populate the GenArk hubs?
Here at UCSC, an internal process maintains a local mirror image of the NCBI genome assembly resources. In essence, there is first a transfer of data with a rsync request, rsync://ftp.ncbi.nlm.nih.gov/genomes/all/GC[AF]/ to a matching local hierarchy of directories. These matching directory structures and naming conventions for files enable scripting procedures to automatically find and process the source files into the formats the UCSC Genome Browser recognizes to visualize data, mainly byte-range accessible binary-indexed versions of the data. A Perl script, doAssemblyHub.pl, manages all the steps of the procedure (https://genome-source.gi.ucsc.edu/gitlist/kent.git/blob/master/src/hg/utils/automation/doAssemblyHub.pl).
So how are gene tracks created for these GenArk hubs?
For the assemblies with GCF accessions, the script uses the supplied data of the NCBI gene annotations to create gene tracks that are provided with those files. A specific gene track type called bigGenePred, https://genome.ucsc.edu/goldenPath/help/bigGenePred.html, allows amino acid displays when zoomed-in at the base level. Likewise, a bigGenePred track is made to display Xeno RefGene data which is computed from a selection of best alignments of RefSeq mRNA sequences from many organisms to the genome, using the BLAT (http://www.kentinformatics.com/) algorithm (blat -noHead -q=rnax -t=dnax -mask=lower target.fa.gz query.fa.gz results.psl). Another bigGenePred track is made using the Augustus gene prediction software (http://bioinf.uni-greifswald.de/augustus/) from the Stanke lab.
What if I don’t find my Assembly in the GenArk collection?
If you can’t find the assembly you want in the GenArk hub collection, but you do already have the GCA/GCF identifier you can email us at our public mailing-list genome@ucsc.soe.edu to request we add the assembly to the GenArk collection. This archived mailing-list is searchable from links on our contacts page, http://genome.ucsc.edu/contacts.html. Alternatively, if you don’t want your request to be public, you can email our private internal mailing-list at genome-www@soe.ucsc.edu. Also, since this original blog post, we created a new assembly request page, you can find details in this 4th GenArk blog post.
What if my assembly doesn’t have a GCA/GCF NCBI accession?
If NCBI does not have a GCA/GCF accession for your assembly then our scripts will not be able to pull the data and generate the GenArk hub. You will need to deposit the assembly at NCBI and notify us once the assembly has become available. You can find directions at NCBI for how to submit new genomes: https://www.ncbi.nlm.nih.gov/assembly/docs/submission/
A future manuscript is also in the works to further detail the background of the GenArk hubs.
This was the final blog in a three-part series about GenArk hubs authored by Brian Lee. The first post focused on how to discover and access the hubs, while the second blog post provided tutorial examples of using the GenArk hubs, such as the BLAT and PCR tools that are available, or how you can send DNA of any Assembly Hubs to External Tools for processing.
If after reading this blog post you have any public questions, please email genome@soe.ucsc.edu. All messages sent to that address are archived on a publicly accessible forum. If your question includes sensitive data, you may send it instead to genome-www@soe.ucsc.edu.
This blog post is the first of three to discuss the Genome Archive (GenArk) assembly hubs. This first post discusses accessing the GenArk hubs, the second post gives examples of using the data, and the third post describes the technical infrastructure behind the hubs.
Let’s start with a real-world story: imagine you are a researcher working on zebrafish, but you are using an alternative strain with unique polymorphic properties. You have a desire to do CRISPR on your particular zebrafish and you already have a FASTA file for the genome assembled into chromosomes, but have no annotations or way to visualize the data yet.
One option to visualize your FASTA would be to independently create a UCSC Assembly Track Hub to work on your zebrafish. Or now that UCSC has developed the Genome Archive (GenArk) system, when you submit your assembly into NCBI’s assembly database, you could contact us directly and request we generate the browser for you behind the scenes. This happened for a specific lab, where they submitted their specific TD5 zebrafish assembly to NCBI, https://www.ncbi.nlm.nih.gov/assembly/GCA_018400075.1, and the result after contacting us was a new assembly hub that could be easily loaded at UCSC with the following link: https://genome.ucsc.edu/h/GCA_018400075.1 In this case, the team at UCSC even helped generate liftOver alignment files between the UCSC zebrafish in this new TD5 zebrafish GenArk Public Hub addition, aiding identification of lifting annotations to the new browser.
So what are the GenArk Assembly hubs?
GenArk hubs are a collection of data files externally hosted from the main UCSC data website enabling browsing new genomes. GenArk genomes have NCBI Genbank assembly accessions starting with either GCA or GCF and the browsers allow visualizing and attaching laboratory-generated data. New software also enables UCSC to dynamically turn on query servers to search GenArk hubs with DNA sequences or test PCR primer pairs. GenArk hubs are part of the UCSC Public Hubs list where UCSC can update the data files with pipelines.
ACCESSING THE DATA
How do I access GenArk Assembly Hubs?
There are multiple ways to access the GenArk hubs, including searching the UCSC Genome Browser’s main gateway page, building direct links to NCBI GCA/GCF assembly accessions, searching the UCSC Public Hubs page, and navigating directly to individual taxonomic group pages.
Browser Gateway Page
The easiest way to find GenArk hubs is to search the species name on the Browser Gateway.
On the Gateway page in the top left box you can search a term such as “dog” and find all the genomes both hosted in our internal databases and in external Public Hubs that have dog in the name. In this image, a search for “dog” returns a top “Dog” match (UCSC database) as well as results for several species in Assembly Track Hubs that match on the term “dog” with the specific labrador dog breed selected from the GenArk Mammal Assemblies Hub (GCF_014441545.1).
Direct GCA/GCF Accession Links
In the situation where you may know the GCF/GCA identifier for an assembly, you can also search that term on the Gateway page or build a short link to directly load the hub. Links to UCSC with a hub (“/h/”) address, such as https://genome.ucsc.edu/h/GCF_000698965.1 will attempt to find and attach a matching final GCF-value, which originates from the NCBI accession, in this case, for an African ostrich assembly. If you don’t find a match, read more below about contacting us.
Public Hubs Page
Another place to find GenArk hubs is on the Public Hubs page where you can enter various terms, like “ostrich”: https://genome.ucsc.edu/cgi-bin/hgHubConnect?hubSearchTerms=ostrich, You can expand the “Search details” to examine matching results. To load a desired hub, use a right-click to display an “Open this assembly” pop-up, or an option to configure individual track settings.
Genomes Menu
Another option to gain an overview of all the GenArk hubs is to click the “Genome Archive GenArk” link available under the “Genomes” menu.
This Genomes menu link will open the GenArk homepage. On the GenArk homepage, a variety of links exist including the line,“Please note: text file listing of 1,600 NCBI/VGP genome assembly hubs.” Clicking that link will open a single text file that lists all available hubs allowing a quick overview: https://hgdownload.soe.ucsc.edu/hubs/UCSC_GI.assemblyHubList.txt
Individual Taxonomic Pages
The GenArk homepage also has links to specific taxonomic groupings hub pages, such as mammals, fishes, or fungi. For instance, a “birds” link, https://hgdownload.soe.ucsc.edu/hubs/birds/index.html, brings you to a webpage with links to launch browsers, along with links to other details for each assembly.
These taxonomic group pages, such as this image of the bird’s page, have links to launch the browser (2nd column: common name and view in browser) and links to the source files (4th column: NCBI assembly).
Access to these taxonomic group pages is also available from the Public Hubs page.
By going to the Description column on the Public Hubs page you can click a link (Bird genome assemblies) to end up at the related taxonomic grouping page. Also of note that on the Public Hubs page, you can click a [+] plus button to expand the list of Assemblies and click one of the GCA/GCF accession links to directly load an assembly.
What if I don’t find my Assembly in the GenArk collection?
If the assembly of interest is not found, please visit our assembly request page. Search that page for your assembly, if there is a “view” link you can launch the existing genome browser. Otherwise, click the “request” button to fill out a form to add your genome of interest.
The assembly request page does require there to already be an existing GCA/GCF identifier. You can also always email us at our public mailing-list genome@ucsc.soe.edu to request we add the assembly to the GenArk collection. This archived mailing-list is searchable from links on our contacts page, http://genome.ucsc.edu/contacts.html. Alternatively, if you don’t want your request to be public, you can email our private internal mailing-list at genome-www@soe.ucsc.edu.
What if my assembly doesn’t have a GCA/GCF NCBI accession?
If NCBI does not have a GCA/GCF accession for your assembly then our scripts will not be able to pull the data and generate the GenArk hub. You will need to deposit the assembly at NCBI and notify us once the assembly has become available. You can find directions at NCBI for how to submit new genomes: https://www.ncbi.nlm.nih.gov/assembly/docs/submission/
The next blog post in this series will provide examples of using the GenArk hubs, such as the BLAT and PCR tools that are available, or how you can send DNA of any Assembly Hubs to External Tools for processing. The final post examines the infrastructure behind the hubs.
This entry written by Brian Lee. If after reading this blog post you have any public questions, please email genome@soe.ucsc.edu. All messages sent to that address are archived on a publicly accessible forum. If your question includes sensitive data, you may send it instead to genome-www@soe.ucsc.edu.
On the Gateway page in the top left box you can search a term such as “dog” and find all the genomes both hosted in our internal databases and in external Public Hubs that have dog in the name. In this image, a search for “dog” returns a top “Dog” match (UCSC database) as well as results for several species in Assembly Track Hubs that match on the term “dog” with the specific labrador dog breed selected from the GenArk Mammal Assemblies Hub (GCF_014441545.1).
