This directory contains the Build 34 finished human genome
assembly (hg16, Jul. 2003). The chromosomal sequences were
assembled by the International Human Genome Project sequencing
centers and verified by NCBI and UCSC. The annotations are from
UCSC and collaborators worldwide.
Files included in this directory:
hg16.2bit - contains the complete human/hg16 genome sequence
in the 2bit file format. While we are providing the .2bit for
this assembly, we will continue to use the .nib files in
the Genome Browser. 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
chromAgp.zip - Description of how the assembly was generated,
unpacking to one file per chromosome.
chromFa.zip - The assembly sequence in one file per chromosome.
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 main assembly is found in the chrN.fa
files, where N is the name of the chromosome. The chrN_random.fa
files contain clones that are not yet finished or cannot be placed
with certainty at a specific place on the chromosome. In some
cases, including the human HLA region on chromosome 6, the
chrN_random.fa files also contain haplotypes that differ from the
main assembly.
chromFaMasked.zip - The assembly sequence in one file per
chromosome. Repeats are masked by capital Ns; non-repeating
sequence is shown in upper case.
chromOut.zip - RepeatMasker .out file for chromosomes. These were
created by RepeatMasker at the -s sensitive setting.
chromTrf.zip - Tandem Repeats Finder locations, filtered to keep
repeats with period of less than or equal to 12, and translated
into one .bed file per chromosome.
contigAgp.zip - Description of how the assembly was generated
from fragments at a contig layout level.
contigFa.zip - The assembly sequence contigs, in one file per NCBI contig.
All contigs are in forward orientation relative to the chromosome.
In some cases, this means that contigs will be reversed relative to
their orientation in the NCBI assembly. Repeats from RepeatMasker
and Tandem Repeats Finder are shown in lower case; non-repeating
sequence is shown in upper case.
contigFaMasked.zip - The assembly sequence contigs, in one file per
contig. Repeats are masked by capital Ns; non-repeating sequence
is shown in upper case.
contigOut.zip - RepeatMasker .out file for contigs. These were
created by RepeatMasker at the -s sensitive setting.
contigTrf.zip - Tandem Repeats Finder locations, filtered to keep
repeats with period less than or equal to 12, and translated into
one .bed file per contig.
est.fa.gz - Human ESTs from GenBank.
This sequence data is updated once a week via automatic GenBank
updates.
liftAll.zip - Offsets of contigs within chromosomes.
mrna.fa.gz - Human mRNA from GenBank.
This sequence data is updated once a week via automatic GenBank
updates.
refMrna.fa.gz - RefSeq mRNA from the same species as the genome.
This sequence data is updated once a week via automatic GenBank
updates.
upstream1000.fa.gz - Sequences 1000 bases upstream of annotated
transcription starts for RefSeq genes with annotated 5' UTRs.
This file is updated weekly so it could be slightly out
of sync with the RefSeq data which is updated daily for most
assemblies.
upstream2000.zip - Same as upstream1000, but 2000 bases.
upstream5000.zip - Same as upstream1000, but 5000 bases.
xenoMrna.fa.gz - All GenBank mRNAs from species other than that of
the genome. This sequence data is updated once a week via automatic
GenBank updates.
hg16.chrom.sizes - Two-column tab-separated text file containing assembly
sequence names and sizes.
----------------------------------------------------------------
If you plan to download a large file or multiple files from this
directory, we recommend that you use ftp rather than downloading the
files via our website. To do so, ftp to hgdownload.cse.ucsc.edu, then
go to the directory goldenPath/hg16/bigZips. To download multiple
files, use the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
All files in this directory are freely available for public use.
Name Last modified Size Description
Parent Directory -
chromAgp.zip 2003-08-01 13:23 531K
chromFa.zip 2003-08-06 09:59 894M
chromFaMasked.zip 2003-08-06 10:20 488M
chromOut.zip 2003-08-06 09:23 151M
chromTrf.zip 2003-08-01 16:08 6.7M
contigAgp.zip 2003-08-01 16:49 609K
contigFa.zip 2003-08-06 11:06 894M
contigFaMasked.zip 2003-08-06 11:27 488M
contigOut.zip 2003-08-06 10:23 150M
contigTrf.zip 2003-08-01 16:58 7.0M
est.fa.gz 2019-10-17 11:01 1.5G
est.fa.gz.md5 2019-10-17 11:01 44
hg16.2bit 2005-06-20 07:22 768M
hg16.2bit.md5 2014-05-07 15:22 44
hg16.chrom.sizes 2003-08-05 10:42 713
hg16.fa.gz 2020-01-23 02:22 895M
liftAll.zip 2003-08-01 16:08 7.0K
mrna.fa.gz 2019-10-17 10:44 370M
mrna.fa.gz.md5 2019-10-17 10:44 45
refMrna.fa.gz 2019-10-17 11:02 80M
refMrna.fa.gz.md5 2019-10-17 11:02 48
upstream1000.fa.gz 2019-10-17 11:03 9.2M
upstream1000.fa.gz.md5 2019-10-17 11:03 53
upstream2000.fa.gz 2019-10-17 11:04 17M
upstream2000.fa.gz.md5 2019-10-17 11:04 53
upstream5000.fa.gz 2019-10-17 11:05 45M
upstream5000.fa.gz.md5 2019-10-17 11:05 53
xenoMrna.fa.gz 2019-10-17 10:53 6.4G
xenoMrna.fa.gz.md5 2019-10-17 10:53 49
xenoRefMrna.fa.gz 2019-10-17 11:02 250M
xenoRefMrna.fa.gz.md5 2019-10-17 11:02 52