Common name: Southeast Asian liver fluke
Taxonomic name: Opisthorchis viverrini, taxonomy ID: 6198
Sequencing/Assembly provider ID: The University of Melbourne
Assembly date: 09 Jul 2014
Assembly type: haploid
Assembly level: Scaffold
Biosample: SAMN00996407
Assembly accession ID: GCF_000715545.1
Assembly FTP location: GCF/000/715/545/GCF_000715545.1_OpiViv1.0
Total assembly nucleotides: 620,452,578
Assembly contig count: 42,216
N50 size: 1,349,843

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.

To download this assembly data, use this rsync command:

  rsync -a -P \
    rsync:// \

  which creates the local directory: ./GCF_000715545.1/
or this wget command:
  wget --timestamping -m -nH -x --cut-dirs=6 -e robots=off -np -k \
    --reject "index.html*" -P "GCF_000715545.1" \

  which creates a local directory: ./GCF_000715545.1/

There is an included hub.txt file in that download data directory to use for your local track hub instance.
Using the genome browser menus: My Data -> Track Hubs
select the My Hubs tab to enter a URL to this hub.txt file to attach this assembly hub to a genome browser.

The html/GCF_000715545.1_OpiViv1.0.description.html page is information for your users to describe this assembly. This WEB page with these instructions is an instance of html/GCF_000715545.1_OpiViv1.0.description.html file.

See also: track hub help documentation.

To operate a blat server on this assembly, in the directory where you have the GCF_000715545.1_OpiViv1.0.2bit file:

gfServer -log=GCF_000715545.1_OpiViv1.0.gfServer.trans.log -ipLog -canStop start \ 76543 -trans -mask GCF_000715545.1_OpiViv1.0.2bit &
gfServer -log=GCF_000715545.1_OpiViv1.0.gfServer.log -ipLog -canStop start \ 76542 -stepSize=5 GCF_000715545.1_OpiViv1.0.2bit &
Adjust the port numbers 76543 76542 and the for your local circumstances.
Typically, port numbers in the range 49152 to 65535 are available for private use as in this case. See also: port registry.

Enter the following specifications in your genomes.txt file:

transBlat 76543
blat 76542
See also: Blat for an Assembly Hub

Search the assembly: