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: 09 Feb 2018
Assembly type: haploid
Assembly level: Chromosome
Biosample: SAMN05181962
Assembly accession ID: GCA_002077035.3
Assembly FTP location: GCA/002/077/035/GCA_002077035.3_NA12878_prelim_3.0
Total assembly nucleotides: 3,088,210,890
Assembly contig count: 2,142
N50 size: 155,131,045

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:// \

  which creates the local directory: ./GCA_002077035.3_NA12878_prelim_3.0/
or this wget command:
  wget --timestamping -m -nH -x --cut-dirs=4 -e robots=off -np -k \
    --reject "index.html*" -P "GCA_002077035.3_NA12878_prelim_3.0" \

  which creates a local directory: ./GCA_002077035.3_NA12878_prelim_3.0/

There is an included GCA_002077035.3_NA12878_prelim_3.0.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_002077035.3_NA12878_prelim_3.0
genomesFile GCA_002077035.3_NA12878_prelim_3.0.genomes.txt
descriptionUrl html/GCA_002077035.3_NA12878_prelim_3.0.description.html
The html/GCA_002077035.3_NA12878_prelim_3.0.description.html page is information for your users to describe this assembly. This WEB page with these instructions is an instance of html/GCA_002077035.3_NA12878_prelim_3.0.description.html file.

To operate a blat server on this assembly, in the directory where you have the GCA_002077035.3_NA12878_prelim_3.0.2bit file:

gfServer -log=GCA_002077035.3_NA12878_prelim_3.0.gfServer.trans.log -ipLog -canStop start \ 76543 -trans -mask GCA_002077035.3_NA12878_prelim_3.0.2bit &
gfServer -log=GCA_002077035.3_NA12878_prelim_3.0.gfServer.log -ipLog -canStop start \ 76542 -stepSize=5 GCA_002077035.3_NA12878_prelim_3.0.2bit &
Adjust the port numbers 76543 76542 and the for your local circumstances.
Enter the following specifications in your genomes.txt file:
transBlat 76543
blat 76542
See also: Blat for an Assembly Hub

Search the assembly: