Common name: human
Taxonomic name: Homo sapiens, taxonomy ID: 9606
Sequencing/Assembly provider ID: T2T Consortium
Assembly date: 24 Jan 2022
Assembly type: haploid
Assembly level: Complete Genome
Biosample: (n/a)
Assembly accession ID: GCA_009914755.4
Assembly FTP location: GCA/009/914/755/GCA_009914755.4_T2T-CHM13v2.0
Total assembly nucleotides: 3,117,292,070
Assembly contig count: 25
N50 size: 150,617,247

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Data file downloads

• hs1.fa.gz fasta sequence
• hs1.chromAlias.txt chromAlias file to relate chromosome names
• hs1.2bit hs1.2bit UCSC 2bit sequence file
• hs1.ncbiRefSeq.gtf.gz NCBI RefSeq genes GTF file
• hs1.ncbiRefSeq.gp.gz NCBI RefSeq genes genePred file
• explore the data download directory at: hgdownload.soe.ucsc.edu/goldenPath/hs1/

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blat service

There is blat service available for this genome assembly. When viewing this assembly in the genome browser, access the blat service via the Tools -> Blat blue navigation bar menu item.

For local command line blat service, access the blat service via the gfClient command line operation.
See also: hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/ to download command line binaries.

To operate this locally, you will need the hs1.2bit file from:

  https://hgdownload.soe.ucsc.edu/goldenPath/hs1/bigZips/

Which can be obtained with rsync via:

  rsync -a -P \
    rsync://hgdownload.soe.ucsc.edu/goldenPath/hs1/bigZips/hs1.2bit ./

With that hs1.2bit file in your working directory where you run this command, for example, a DNA query with your DNA sequence in the file: someDna.fa with result in the file: hs1.someDna.psl

gfClient -t=dna -q=dna -genome=hs1 -genomeDataDir=hs1 \
    dynablat-01.soe.ucsc.edu 4040 ./ someDna.fa hs1.someDna.psl

For a protein fasta query with your protein sequence in the file: someProtein.faa with result in the file: hs1.someProtein.psl

gfClient -t=dnax -q=prot  -genome=hs1 -genomeDataDir=hs1 \
    dynablat-01.soe.ucsc.edu 4040 ./ someProtein.faa hs1.someProtein.psl

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Search the assembly:

• By position or search term: Use the "position or search term" box to find areas of the genome associated with many different attributes, such as a specific chromosomal coordinate range; mRNA, EST, or STS marker names; or keywords from the GenBank description of an mRNA. More information, including sample queries.
• By gene name: Type a gene name into the "search term" box, choose your gene from the drop-down list, then press "submit" to go directly to the assembly location associated with that gene. More information. To avoid case sensitivity issues, always use fully lower case gene names.
• By track type: Click the "track search" button to find Genome Browser tracks that match specific selection criteria. More information.

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