This is the human assembly made by the T2T project called CHM13 V2.0. It
contains sequences for centromeres and other difficult to sequence regions and has no
gaps. If you are new to genomics or unsure about which assembly to use,
note that the improvements concern regions of the genome that are not
yet important for most analyses or diagnostic purposes.
This is not the human genome reference sequence released by the Genome
Reference Consortium GRCh38 (aka hg38), which is used by most databases,
aligners and diagnostics labs at the moment. If you are looking for the
current human reference sequence then you may want to use
https://hgdownload.ucsc.edu/goldenPath/hg38/bigZips/ rather than basing your
analysis on CHM13.
Files:
hs1.fa.gz - "Soft-masked" assembly CHM13 sequence in one file.
Repeats from RepeatMasker and Tandem Repeats Finder (with period of 12 or
less) are shown in lower case; non-repeating sequence is shown in upper
case.
hs1.2bit - contains the complete human CHM13 genome sequence
in the 2bit file format. Repeats from RepeatMasker and Tandem Repeats
Finder (with period of 12 or less) are shown in lower case; non-repeating
sequence is shown in upper case. The utility program, twoBitToFa (available
from the kent src tree), can be used to extract .fa file(s) from
this file. A pre-compiled version of the command line tool can be
found at:
http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
See also:
http://genome.ucsc.edu/admin/git.html
http://genome.ucsc.edu/admin/jk-install.html
hs1.repeatMasker.out - RepeatMasker .out file. RepeatMasker was run with the
-s (sensitive) setting.
hs1.repeatMasker.version.txt - version of repeatmasker that was used.
genes/hs1.ncbiRefSeq.gp.gz - gene annotations made by NCBI RefSeq in UCSC genePred format.
genes/hs1.ncbiRefSeq.gtf.gz - gene annotations made by NCBI RefSeq in GFF/GTF format.
Name Last modified Size Description
Parent Directory -
genes/ 2023-08-30 15:16 -
THIS_IS_GENOME_ASSEMBLY_T2T-CHM13v2.0 2022-07-18 12:06 0
hs1.chrom.sizes.txt 2022-06-22 21:16 375
md5sum.txt 2022-09-15 11:21 658
hs1.chromAlias.txt 2022-07-18 11:38 866
hs1.repeatMasker.version.txt 2022-02-04 10:35 922
hs1.2bit.bpt 2022-07-16 14:50 3.3K
GCA_009914755.4_assembly_report.txt 2022-08-11 03:26 3.4K
hs1.chromAlias.bb 2022-07-18 11:38 43K
hs1.repeatMasker.out.gz 2022-07-18 11:48 173M
hs1.2bit 2022-07-16 14:27 775M
hs1.fa.gz 2022-07-18 12:08 930M
hs1.untrans.gfidx 2022-07-16 14:32 2.1G
hs1.trans.gfidx 2022-07-16 14:33 4.6G