Common name: human
Taxonomic name: Homo sapiens, taxonomy ID: 9606
Sequencing/Assembly provider ID: The Genome Institute at Washington University School of Medicine
Assembly date: 24 Apr 2018
Assembly type: haploid
Assembly level: Contig
Biosample: SAMN05603847
Assembly accession ID: GCA_003070785.1
Assembly FTP location: GCA/003/070/785/GCA_003070785.1_HG02059_prelim_1.0
Total assembly nucleotides: 2,898,275,003
Assembly contig count: 3,180
N50 size: 25,293,151


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.
See also: track hub help documentation.

To download this assembly data, use this rsync command:

  rsync -a -P \
    rsync://hgdownload.soe.ucsc.edu/hubs/globalReference/genomes/GCA_003070785.1_HG02059_prelim_1.0/ \
      ./GCA_003070785.1_HG02059_prelim_1.0/

  which creates the local directory: ./GCA_003070785.1_HG02059_prelim_1.0/
or this wget command:
  wget --timestamping -m -nH -x --cut-dirs=4 -e robots=off -np -k \
    --reject "index.html*" -P "GCA_003070785.1_HG02059_prelim_1.0" \
       https://hgdownload.soe.ucsc.edu/hubs/globalReference/genomes/GCA_003070785.1_HG02059_prelim_1.0/

  which creates a local directory: ./GCA_003070785.1_HG02059_prelim_1.0/

There is an included GCA_003070785.1_HG02059_prelim_1.0.genomes.txt file in that download data to use for your local track hub instance.
You will need to add a hub.txt file to point to this genomes.txt file.
Something like:
hub myLocalHub
shortLabel myLocalHub
longLabel genome assembly GCA_003070785.1_HG02059_prelim_1.0
genomesFile GCA_003070785.1_HG02059_prelim_1.0.genomes.txt
email yourEmail@yourdomain.edu
descriptionUrl html/GCA_003070785.1_HG02059_prelim_1.0.description.html
The html/GCA_003070785.1_HG02059_prelim_1.0.description.html page is information for your users to describe this assembly. This WEB page with these instructions is an instance of html/GCA_003070785.1_HG02059_prelim_1.0.description.html file.


To operate a blat server on this assembly, in the directory where you have the GCA_003070785.1_HG02059_prelim_1.0.2bit file:

gfServer -log=GCA_003070785.1_HG02059_prelim_1.0.gfServer.trans.log -ipLog -canStop start \
    yourserver.domain.edu 76543 -trans -mask GCA_003070785.1_HG02059_prelim_1.0.2bit &
gfServer -log=GCA_003070785.1_HG02059_prelim_1.0.gfServer.log -ipLog -canStop start \
    yourserver.domain.edu 76542 -stepSize=5 GCA_003070785.1_HG02059_prelim_1.0.2bit &
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 76542
See also: Blat for an Assembly Hub


Search the assembly: