Common name: tufted duck
Taxonomic name: Aythya fuligula, taxonomy ID: 219594
Sequencing/Assembly provider ID: Vertebrate Genomes Project
Assembly date: 31 Dec 2019
Assembly type: haploid (principal pseudohaplotype of diploid)
Assembly level: Chromosome
Biosample: SAMN12621346
Assembly accession ID: GCA_009819795.1
Assembly FTP location: GCF/009/819/795/GCF_009819795.1_bAytFul2.pri
Total assembly nucleotides: 1,127,004,725
Assembly contig count: 105
N50 size: 85,905,639
Download files for this assembly hub:
To use the data from this assembly for a local hub instance at your
institution, download these data as indicated by these instructions.
To download this assembly data, use this rsync command:
rsync -a -P \ rsync://hgdownload.soe.ucsc.edu/hubs/GCF/009/819/795/GCF_009819795.1/ \ ./GCF_009819795.1/ which creates the local directory: ./GCF_009819795.1/or this wget command:
wget --timestamping -m -nH -x --cut-dirs=6 -e robots=off -np -k \ --reject "index.html*" -P "GCF_009819795.1" \ https://hgdownload.soe.ucsc.edu/hubs/GCF/009/819/795/GCF_009819795.1/ which creates a local directory: ./GCF_009819795.1/
There is an included hub.txt file in that download
data directory to use for your local track hub instance.
Using the genome browser menus: My Data -> Track Hubs
select the My Hubs tab to enter a URL
to this hub.txt file to attach this assembly hub to a genome browser.
The html/GCF_009819795.1_bAytFul2.pri.description.html page is information for your users to describe this assembly. This WEB page with these instructions is an instance of html/GCF_009819795.1_bAytFul2.pri.description.html file.
See also: track hub help documentation.
To operate a blat server on this assembly, in the directory where you have the GCF_009819795.1_bAytFul2.pri.2bit file:
gfServer -log=GCF_009819795.1_bAytFul2.pri.gfServer.trans.log -ipLog -canStop start \ yourserver.domain.edu 76543 -trans -mask GCF_009819795.1_bAytFul2.pri.2bit & gfServer -log=GCF_009819795.1_bAytFul2.pri.gfServer.log -ipLog -canStop start \ yourserver.domain.edu 76542 -stepSize=5 GCF_009819795.1_bAytFul2.pri.2bit &Adjust the port numbers 76543 76542 and the yourserver.domain.edu for your local circumstances.
Enter the following specifications in your genomes.txt file:
transBlat yourserver.domain.edu 76543 blat yourserver.domain.edu 76542See also: Blat for an Assembly Hub
Search the assembly: