Ornithorhynchus anatinus (Photo courtesy of CC BY-NC 2.0 Trevira1 (flickr)) |
Common name: duckbill platypus
Taxonomic name: Ornithorhynchus anatinus, taxonomy ID: 9258
Sequencing/Assembly provider ID: Vertebrate Genomes Project
Vertebrate Genomes Project information: Ornithorhynchus anatinus
Assembly date: 07 Feb 2019
Assembly type: haploid
Assembly level: Chromosome
Biosample: SAMN08537700
Assembly accession ID: GCA_004115215.2
Assembly FTP location: GCF/004/115/215/GCF_004115215.1_mOrnAna1.p.v1
Total assembly nucleotides: 1,858,552,590
Assembly contig count: 305
N50 size: 83,338,043
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/VGP/genomes/GCF_004115215.1_mOrnAna1.p.v1/ ./GCF_004115215.1_mOrnAna1.p.v1/ which creates the local directory: ./GCF_004115215.1_mOrnAna1.p.v1/or this wget command:
wget --timestamping -m -nH -x --cut-dirs=4 -e robots=off -np -k \ --reject "index.html*" -P "GCF_004115215.1_mOrnAna1.p.v1" \ https://hgdownload.soe.ucsc.edu/hubs/VGP/genomes/GCF_004115215.1_mOrnAna1.p.v1/ which creates a local directory: ./GCF_004115215.1_mOrnAna1.p.v1/
hub myLocalHub shortLabel myLocalHub longLabel genomes from Vertebrate Genomes Project assemblies genomesFile GCF_004115215.1_mOrnAna1.p.v1.genomes.txt email yourEmail@yourdomain.edu descriptionUrl html/GCF_004115215.1_mOrnAna1.p.v1.description.htmlThe html/GCF_004115215.1_mOrnAna1.p.v1.description.html page is information for your users to describe this assembly. This WEB page with these instructions is an instance of html/GCF_004115215.1_mOrnAna1.p.v1.description.html file.
To operate a blat server on this assembly, in the directory where you have the GCF_004115215.1_mOrnAna1.p.v1.2bit file:
gfServer -log=GCF_004115215.1_mOrnAna1.p.v1.gfServer.trans.log -ipLog -canStop start \ yourserver.domain.edu 76543 -trans -mask GCF_004115215.1_mOrnAna1.p.v1.2bit & gfServer -log=GCF_004115215.1_mOrnAna1.p.v1.gfServer.log -ipLog -canStop start \ yourserver.domain.edu 76542 -stepSize=5 GCF_004115215.1_mOrnAna1.p.v1.2bit &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: