Takifugu rubripes (Photo courtesy of CC BY-SA 2.5 OpenCage (wikimedia)) |
Common name: tiger puffer
Taxonomic name: Takifugu rubripes, taxonomy ID: 31033
Sequencing/Assembly provider ID: SC
Vertebrate Genomes Project information: Takifugu rubripes
Assembly date: 05 Jun 2019
Assembly type: haploid
Assembly level: Chromosome
Biosample: SAMEA104384834
Assembly accession ID: GCA_901000725.2
Assembly FTP location: GCF/901/000/725/GCF_901000725.2_fTakRub1.2
Total assembly nucleotides: 384,126,662
Assembly contig count: 128
N50 size: 16,705,553
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_901000725.2_fTakRub1.2/ ./GCF_901000725.2_fTakRub1.2/ which creates the local directory: ./GCF_901000725.2_fTakRub1.2/or this wget command:
wget --timestamping -m -nH -x --cut-dirs=4 -e robots=off -np -k \ --reject "index.html*" -P "GCF_901000725.2_fTakRub1.2" \ https://hgdownload.soe.ucsc.edu/hubs/VGP/genomes/GCF_901000725.2_fTakRub1.2/ which creates a local directory: ./GCF_901000725.2_fTakRub1.2/
hub myLocalHub shortLabel myLocalHub longLabel genomes from Vertebrate Genomes Project assemblies genomesFile GCF_901000725.2_fTakRub1.2.genomes.txt email yourEmail@yourdomain.edu descriptionUrl html/GCF_901000725.2_fTakRub1.2.description.htmlThe html/GCF_901000725.2_fTakRub1.2.description.html page is information for your users to describe this assembly. This WEB page with these instructions is an instance of html/GCF_901000725.2_fTakRub1.2.description.html file.
To operate a blat server on this assembly, in the directory where you have the GCF_901000725.2_fTakRub1.2.2bit file:
gfServer -log=GCF_901000725.2_fTakRub1.2.gfServer.trans.log -ipLog -canStop start \ yourserver.domain.edu 76543 -trans -mask GCF_901000725.2_fTakRub1.2.2bit & gfServer -log=GCF_901000725.2_fTakRub1.2.gfServer.log -ipLog -canStop start \ yourserver.domain.edu 76542 -stepSize=5 GCF_901000725.2_fTakRub1.2.2bit &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: