Mus musculus (house mouse)
(Photo courtesy of The Jackson Laboratory)

Common name: mouse
Taxonomic name: Mus musculus (house mouse), taxonomy ID: 10090
Sequencing/Assembly provider ID: Wellcome Trust Sanger Institute
Assembly date: 26 Apr 2016
Assembly type: haploid
Assembly level: Chromosome
Biosample: SAMN04489828
Assembly accession ID: GCA_001624745.1
Assembly FTP location: GCA_001624745.1_NZO_HlLtJ_v1
Total assembly nucleotides: 2,699,267,296
Assembly contig count: 7,022
N50 size: 132,960,827

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 these data, issue this wget command:

wget --timestamping -m -nH -x --cut-dirs=5 -e robots=off -np -k \
   --reject "index.html*" -P "GCA_001624745.1_NZO_HlLtJ_v1" \
to download the files for this assembly,
creating the local directory: "GCA_001624745.1_NZO_HlLtJ_v1"

There is an included GCA_001624745.1_NZO_HlLtJ_v1.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 genomes from RefSeq assemblies
genomesFile GCA_001624745.1_NZO_HlLtJ_v1.genomes.txt
descriptionUrl html/GCA_001624745.1_NZO_HlLtJ_v1.description.html
The html/GCA_001624745.1_NZO_HlLtJ_v1.description.html page is information for your users to describe this assembly. This WEB page with these instructions is an instance of html/GCA_001624745.1_NZO_HlLtJ_v1.description.html file.

To operate a blat server on this assembly, in the directory where you have the GCA_001624745.1_NZO_HlLtJ_v1.2bit file:

gfServer -log=GCA_001624745.1_NZO_HlLtJ_v1.gfServer.trans.log -ipLog -canStop start \ 76543 -trans -mask GCA_001624745.1_NZO_HlLtJ_v1.2bit &
gfServer -log=GCA_001624745.1_NZO_HlLtJ_v1.gfServer.log -ipLog -canStop start \ 76542 -stepSize=5 GCA_001624745.1_NZO_HlLtJ_v1.2bit &
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: