Common name: yellow fever mosquito
Taxonomic name: Aedes aegypti, taxonomy ID: 7159
Sequencing/Assembly provider ID: Aedes aegypti Genome Working Group (AGWG)
Assembly date: 22 Jun 2017
Assembly type: haploid-with-alt-loci
Assembly level: Chromosome
Assembly accession ID: GCF_002204515.2
Assembly FTP location: GCF/002/204/515/GCF_002204515.2_AaegL5.0
Total assembly nucleotides: 1,278,732,104
Assembly contig count: 2,310
N50 size: 409,777,670
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://hgdownload.soe.ucsc.edu/hubs/GCF/002/204/515/GCF_002204515.2/ \ ./GCF_002204515.2/ which creates the local directory: ./GCF_002204515.2/or this wget command:
wget --timestamping -m -nH -x --cut-dirs=6 -e robots=off -np -k \ --reject "index.html*" -P "GCF_002204515.2" \ https://hgdownload.soe.ucsc.edu/hubs/GCF/002/204/515/GCF_002204515.2/ which creates a local directory: ./GCF_002204515.2/
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_002204515.2_AaegL5.0.description.html page is information for your users to describe this assembly. This WEB page with these instructions is an instance of html/GCF_002204515.2_AaegL5.0.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_002204515.2_AaegL5.0.2bit file:
gfServer -log=GCF_002204515.2_AaegL5.0.gfServer.trans.log -ipLog -canStop start \ yourserver.domain.edu 76543 -trans -mask GCF_002204515.2_AaegL5.0.2bit & gfServer -log=GCF_002204515.2_AaegL5.0.gfServer.log -ipLog -canStop start \ yourserver.domain.edu 76542 -stepSize=5 GCF_002204515.2_AaegL5.0.2bit &Adjust the port numbers 76543 76542 and the yourserver.domain.edu for your local circumstances.
Enter the following specifications in your genomes.txt file:
transBlat yourserver.domain.edu 76543 blat yourserver.domain.edu 76542See also: Blat for an Assembly Hub
Search the assembly: