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/

  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 &

Enter the following specifications in your genomes.txt file:

transBlat yourserver.domain.edu 76543
blat yourserver.domain.edu 76542

Search the assembly:

• By position or search term: Use the "position or search term" box to find areas of the genome associated with many different attributes, such as a specific chromosomal coordinate range; mRNA, EST, or STS marker names; or keywords from the GenBank description of an mRNA. More information, including sample queries.
• By gene name: Type a gene name into the "search term" box, choose your gene from the drop-down list, then press "submit" to go directly to the assembly location associated with that gene. More information.
• By track type: Click the "track search" button to find Genome Browser tracks that match specific selection criteria. More information.