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

Data file downloads

hs1.fa.gz fasta sequence
hs1.chromAlias.txt hs1.chromAlias.txt chromAlias file to relate chromosome names
hs1.2bit hs1.2bit UCSC 2bit sequence file
hs1.20220412.ncbiRefSeq.gtf.gzhs1.110.20220412.gtf.gz NCBI RefSeq genes GTF file version 110.20220412
hs1.augustus.gtf.gz gene GTF file
hs1.xenoRefGene.gtf.gz gene GTF file
catLiftOffGenesV1.gff3.gz gene GFF3 file
catLiftOffGenesV1.gtf.gz gene GTF file
pre-computed indices for alignment programs: bowtie2, bwa-mem2, hisat2, minimap2
explore the data download directory at: hgdownload.soe.ucsc.edu/goldenPath/hs1/

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

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.