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: 02 Jul 2018
Assembly type: haploid
Assembly level: Contig
Biosample: SAMN05603729
Assembly accession ID: GCA_002209525.2
Assembly FTP location: GCA/002/209/525/GCA_002209525.2_HG01352_prelim_2.1
Total assembly nucleotides: 2,884,526,810
Assembly contig count: 3,162
N50 size: 21,644,977
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_002209525.2_HG01352_prelim_2.1/ \
./GCA_002209525.2_HG01352_prelim_2.1/
which creates the local directory: ./GCA_002209525.2_HG01352_prelim_2.1/
or this wget command:
wget --timestamping -m -nH -x --cut-dirs=4 -e robots=off -np -k \
--reject "index.html*" -P "GCA_002209525.2_HG01352_prelim_2.1" \
https://hgdownload.soe.ucsc.edu/hubs/globalReference/genomes/GCA_002209525.2_HG01352_prelim_2.1/
which creates a local directory: ./GCA_002209525.2_HG01352_prelim_2.1/
hub myLocalHub shortLabel myLocalHub longLabel genome assembly GCA_002209525.2_HG01352_prelim_2.1 genomesFile GCA_002209525.2_HG01352_prelim_2.1.genomes.txt email yourEmail@yourdomain.edu descriptionUrl html/GCA_002209525.2_HG01352_prelim_2.1.description.htmlThe html/GCA_002209525.2_HG01352_prelim_2.1.description.html page is information for your users to describe this assembly. This WEB page with these instructions is an instance of html/GCA_002209525.2_HG01352_prelim_2.1.description.html file.
To operate a blat server on this assembly, in the directory where you have the GCA_002209525.2_HG01352_prelim_2.1.2bit file:
gfServer -log=GCA_002209525.2_HG01352_prelim_2.1.gfServer.trans.log -ipLog -canStop start \
yourserver.domain.edu 76543 -trans -mask GCA_002209525.2_HG01352_prelim_2.1.2bit &
gfServer -log=GCA_002209525.2_HG01352_prelim_2.1.gfServer.log -ipLog -canStop start \
yourserver.domain.edu 76542 -stepSize=5 GCA_002209525.2_HG01352_prelim_2.1.2bit &
Adjust the port numbers 76543 76542 and the
yourserver.domain.edu for your local circumstances.transBlat yourserver.domain.edu 76543 blat yourserver.domain.edu 76542See also: Blat for an Assembly Hub
Search the assembly: