This directory contains the Build 36.1 finished human genome assembly
(hg18, Mar. 2006). The chromosomal sequences were assembled by
the International Human Genome Project sequencing centers.
Files included in this directory:
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. Repeat masking was done using the following
RepeatMasker/RepBase versions: RepBase Update 9.11, RM database
version 20050112. 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.
chromOut.RM3.2.7.zip - RepeatMasker (v3.2.7) .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.
hg18.2bit - hg18.2bit contains the complete hg18 Human Genome
in the 2bit format. A utility program, twoBitToFa (available
from our src tree), can be used to extract .fa file(s) from
this file.
hg18.RM.tbl.tar.gz - the RepeatMasker .tbl file output. Each file
in this tar file is for one chunk of contig sequence used during
the RepeatMasker operation, for example:
1/NT_004321/NT_004321_0.fa.tbl
There are 5990 of these chunks of contig sequences, their coordinate
coorrespondence to contig coordinates can be found in the
hg18.RM.lft.tar.gz lift files.
hg18.RM.lft.tar.gz - lift files to lift the hg18.RM.tbl coordinates to
contig coordinates.
est.fa.gz - Human ESTs in 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 - GenBank mRNAs from species other than that of
the genome. This sequence data is updated once a week via automatic
GenBank updates.
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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 hgdownload.cse.ucsc.edu
user name: anonymous
password: <your email address>
go to the directory goldenPath/hg18/bigZips
To download multiple files from the UNIX command line, use the "mget" command.
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
Use the "prompt" command to toggle the interactive mode if you do not want
to be prompted for each file that you download.
All the files in this directory are freely available for public use.
Name Last modified Size Description
Parent Directory -
xenoMrna.fa.gz 2019-10-17 06:31 6.4G
est.fa.gz 2019-10-17 06:40 1.5G
hg18.fa.gz 2020-01-23 02:22 900M
chromFa.zip 2006-02-03 11:05 899M
contigFa.zip 2006-02-03 11:27 898M
hg18.2bit 2005-12-20 10:33 770M
contigFaMasked.zip 2006-02-03 11:35 488M
chromFaMasked.zip 2006-02-03 11:12 487M
mrna.fa.gz 2019-10-17 06:22 370M
xenoRefMrna.fa.gz 2019-10-17 06:41 250M
chromOut.RM3.2.7.zip 2009-02-05 10:10 162M
chromOut.zip 2006-02-03 10:51 153M
contigOut.zip 2006-02-03 11:14 152M
refMrna.fa.gz 2019-10-17 06:41 80M
upstream5000.fa.gz 2019-10-17 06:43 46M
upstream2000.fa.gz 2019-10-17 06:43 18M
upstream1000.fa.gz 2019-10-17 06:42 9.4M
contigTrf.zip 2006-02-03 11:35 7.0M
chromTrf.zip 2006-02-03 11:35 6.8M
hg18.RM.tbl.tar.gz 2008-11-10 13:55 1.3M
contigAgp.zip 2006-02-03 11:12 596K
chromAgp.zip 2006-04-06 09:45 537K
hg18.RM.lft.tar.gz 2008-11-10 14:08 41K
liftAll.zip 2006-02-03 11:35 5.5K
hg18.chrom.sizes 2005-12-06 16:34 855
md5sum.txt 2009-02-05 10:25 734
upstream5000.fa.gz.md5 2019-10-17 06:43 53
upstream2000.fa.gz.md5 2019-10-17 06:43 53
upstream1000.fa.gz.md5 2019-10-17 06:42 53
xenoRefMrna.fa.gz.md5 2019-10-17 06:41 52
xenoMrna.fa.gz.md5 2019-10-17 06:32 49
refMrna.fa.gz.md5 2019-10-17 06:41 48
mrna.fa.gz.md5 2019-10-17 06:22 45
est.fa.gz.md5 2019-10-17 06:40 44