Common name: Anna's hummingbird
Taxonomic name: Calypte anna, taxonomy ID: 9244
Sequencing/Assembly provider ID: Vertebrate Genomes Project
Assembly date: 16 May 2019
Assembly type: haploid (principal pseudohaplotype of diploid)
Assembly level: Chromosome
Biosample: SAMN02265252
Assembly accession ID: GCA_003957555.2
Assembly FTP location: GCA/003/957/555/GCA_003957555.2_bCalAnn1_v1.p
Total assembly nucleotides: 1,059,706,240
Assembly contig count: 160
N50 size: 74,081,004


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/GCA/003/957/555/GCA_003957555.2/ \
      ./GCA_003957555.2/

  which creates the local directory: ./GCA_003957555.2/
or this wget command:
  wget --timestamping -m -nH -x --cut-dirs=6 -e robots=off -np -k \
    --reject "index.html*" -P "GCA_003957555.2" \
       https://hgdownload.soe.ucsc.edu/hubs/GCA/003/957/555/GCA_003957555.2/

  which creates a local directory: ./GCA_003957555.2/

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/GCA_003957555.2_bCalAnn1_v1.p.description.html page is information for your users to describe this assembly. This WEB page with these instructions is an instance of html/GCA_003957555.2_bCalAnn1_v1.p.description.html file.

See also: track hub help documentation.


To operate a blat server on this assembly, in the directory where you have the GCA_003957555.2_bCalAnn1_v1.p.2bit file:

gfServer -log=GCA_003957555.2_bCalAnn1_v1.p.gfServer.trans.log -ipLog -canStop start \
    yourserver.domain.edu 76543 -trans -mask GCA_003957555.2_bCalAnn1_v1.p.2bit &
gfServer -log=GCA_003957555.2_bCalAnn1_v1.p.gfServer.log -ipLog -canStop start \
    yourserver.domain.edu 76542 -stepSize=5 GCA_003957555.2_bCalAnn1_v1.p.2bit &
Adjust the port numbers 76543 76542 and the yourserver.domain.edu for your local circumstances.
Typically, port numbers in the range 49152 to 65535 are available for private use as in this case. See also: IANA.org port registry.

Enter the following specifications in your genomes.txt file:

transBlat yourserver.domain.edu 76543
blat yourserver.domain.edu 76542
See also: Blat for an Assembly Hub


Search the assembly: