Sequence and Annotation Downloads
This page contains links to sequence and annotation downloads for the genome assemblies
featured in the UCSC Genome Browser. Downloads are also available via the Genome
Browser FTP server. For
access to the most recent assembly of each genome, see the
current genomes directory. To query and download data
in JSON format, use our
JSON API.
To view descriptions of annotations, use
the "describe table schema" button in the
Table Browser.
Previous versions of certain data are available from our
track archive.
All tables in the Genome Browser are freely usable for any purpose except as indicated in the
README.txt files in the download directories. To view restrictions specific to a particular data
set, click on the corresponding download link and review the README text. These data were
contributed by many researchers, as listed on the Genome Browser
credits page. Please acknowledge the
contributor(s) of the data you use.
Human
Mouse
Mammals
Other vertebrates
Deuterostomes
Insects
Nematodes
Other genomes
Other downloads
Source and utilities downloads
The source for the Genome Browser, Blat, liftOver and other utilities is free for non-profit
academic research and for personal use. For information on commercial licensing, see the
Genome Browser and
Blat licensing requirements.
The source and executables for several of these products can be downloaded or purchased from our
online store.
Mirroring the Genome Browser
Precompiled executable binaries are available for installing a local mirrored copy of the Genome
Browser website on your web server, eliminating the need to compile the entire source tree.
If you encounter difficulties with slow download speeds, try using
UDT Enabled Rsync (UDR), which
improves the throughput of large data transfers over long distances. The 32-bit and 64-bit versions
can be downloaded here.
Utilities
The utilities directory offers downloads of
pre-compiled standalone binaries for:
-
LiftOver (which may also be accessed via the
web version). The over.chain liftOver
conversion files are located in the individual assembly download sections.
-
Blat
-
Other command-line utilities
Note about 'permission denied' error:
In order for your computer to run a freshly downloaded utility, you will need to update the file
system permissions to allow your operating system to run the program.
To make utilities usable, turn on its 'executable'
bit:
$ chmod +x ./filePath/utility_name
$ ./filePath/utility_name
Example:
$ chmod +x /home/user/liftover/liftOver
See also:
http://en.wikipedia.org/wiki/Chmod
Please review the userApps
README
for information on fetching specific directories from the kent source tree or downloading
userApps.src.tgz to install all kent utilities.
Note that commercial download and installation of the Blat and In-Silico PCR software requires
a licence, which may be obtained from Kent Informatics.
Human genome
Dec. 2013 (GRCh38/hg38)
Feb. 2009 (GRCh37/hg19)
Mar. 2006 (NCBI36/hg18)
-
Data
and annotations
May 2004 (NCBI35/hg17)
-
Data
and annotations
Jul. 2003 (NCBI34/hg16)
-
Data
and annotations
Apr. 10, 2003 (hg15)
-
Data
and annotations
Nov. 14, 2002 (hg13)
-
Data
and annotations
Jun. 28, 2002 (hg12)
-
Data
and annotations
Apr. 5, 2002 (hg11)
-
Data
and annotations
Dec. 22, 2001 (hg10)
-
Data
and annotations
Aug. 6, 2001 (hg8)
-
Data
and annotations
Apr. 1, 2001 (hg7)
-
Data
and annotations
Dec. 12, 2000 (hg6)
-
Data
and annotations
Oct. 7, 2000 (hg5)
-
Data
and annotations
Oct. 7, 2000 preliminary version
Sep. 5, 2000 (hg4)
-
Data
and annotations
Jun. 15, 2000
May 24, 2000
Older human data and documentation
Alpaca genome
Mar. 2013 (Vicugna_pacos-2.0.1/vicPac2)
Jul. 2008 (Broad/vicPac1)
African clawed frog
Aug. 2016 (Xenopus_laevis_v2)/xenLae2)
American alligator
Aug. 2012 (allMis0.2/allMis1)
Armadillo genome
Dec. 2011 (Baylor/dasNov3)
Atlantic cod genome
May 2010 (Genofisk GadMor_May2010/gadMor1)
Baboon genome
Apr. 2017 (Panu_3.0/papAnu4)
Mar. 2012 (Baylor Panu_2.0/papAnu2)
Nov. 2008 (Baylor Pham_1.0/papHam1)
Bison genome
Oct. 2014 (Bison_UMD1.0/bisBis1)
Bonobo genome
May 2020 (Mhudiblu_PPA_v0/panPan3)
Aug. 2015 (MPI-EVA panpan1.1/panPan2)
May 2012 (Max-Planck/panPan1)
Brown kiwi genome
Jun. 2015 (MPI-EVA AptMant0/aptMan1)
Budgerigar genome
Sep. 2011 (WUSTL v6.3/melUnd1)
Bushbaby genome
Mar. 2011 (Broad/otoGar3)
Cat genome
Nov. 2017 (Felis_catus_9.0/felCat9)
Nov. 2014 (ICGSC Felis_catus_8.0/felCat8)
Sep. 2011 (ICGSC Felis_catus 6.2/felCat5)
Dec. 2008 (NHGRI/GTB V17/felCat4)
Mar. 2006 (Broad/felCat3)
Chicken genome
Mar. 2018 (Gallus_gallus-6.0/galGal6)
Dec. 2015 (Gallus_gallus-5.0/galGal5)
Nov. 2011 (ICGSC Gallus_gallus-4.0/galGal4)
May 2006 ((WUGSC 2.1/galGal3)
Feb. 2004 (WUGSC 1.0/galGal2)
Chimpanzee genome
Jan. 2018 (Clint_PTRv2/panTro6)
May. 2016 (Pan_tro 3.0/panTro5)
Feb. 2011 (SAC 2.1.4/panTro4
Oct. 2010 (CGSC 2.1.3/panTro3)
Mar. 2006 (CGSC 2.1/panTro2)
Nov. 2003 (CGSC 1.1/panTro1)
Chinese hamster genome
Jun. 2017 (CHOK1S_HZDv1/criGriChoV2)
Jul. 2013 (C_griseus_v1.0/criGri1)
Aug. 2011 (CriGri_1.0/criGriChoV1)
Chinese pangolin genome
Aug. 2014 (M_pentadactyla-1.1.1/manPen1)
Coelacanth genome
Aug. 2011 (LatCha1/latCha1)
Cow genome
Apr. 2018 (ARS-UCD1.2/bosTau9)
Jun. 2014 (UMD_3.1.1/bosTau8)
Oct. 2011 (Btau_4.6.1/bosTau7)
Nov. 2009 (Bos_taurus_UMD_3.1/bosTau6)
Apr. 2009 (bosTau5)
Oct. 2007 (Baylor 4.0/bosTau4)
Aug. 2009 (bosTauMd3)
Aug. 2006 (Baylor 3.1/bosTau3)
Mar. 2005 (Baylor 2.0/bosTau2)
May 2004 (bosTau1)
Crab-eating macaque genome
Jun. 2013 (Macaca_fascicularis_5.0/macFas5)
Dog genome
May 2019 (UMICH_Zoey_3.1/canFam5)
Mar. 2020 (UU_Cfam_GSD_1.0/canFam4)
Sep. 2011 (Broad CanFam3.1/canFam3)
May 2005 (Broad/canFam2)
Jul. 2004 (Broad/canFam1)
Dolphin genome
Oct. 2011 (Baylor Ttru_1.4/turTru2)
Elephant genome
Jul. 2009 (Broad/loxAfr3)
May 2005 (loxAfr1/loxAfr1)
Elephant shark genome
Dec. 2013 (Callorhinchus_milii-6.1.3/calMil1)
Ferret genome
Apr. 2011 (MusPutFur1.0/musFur1)
Fugu genome
Oct. 2011 (fugu5/fr3)
Oct. 2004 (JGI V4.0/fr2)
Aug. 2002 (fugu/fr1)
Gibbon genome
Oct. 2012 (Nleu_3.0/nomLeu3)
Jun. 2011 (iGGSC Nleu1.1/nomLeu2)
Jan. 2010 (GGSC Nleu1.0/nomLeu1)
Garter snake genome
Jun. 2015 (Thanmnophis_sirtalis-6.0/thaSir1)
Golden eagle genome
Oct. 2014 (aquChr-1.0.2/aquChr2)
Golden snub-nosed monkey genome
Oct. 2014 (Rrox_v1/rhiRox1)
Gorilla genome
Aug. 2019 (Kamilah_GGO_v0/gorGor6)
Mar. 2016 (GMSRT3/gorGor5)
Dec 2014 (gorGor4.1/gorGor4)
May 2010 (gorGor3.1/gorGor3)
Green monkey genome
Mar 2014 (Chlorocebus_sabeus 1.1/chlSab2)
Guinea pig genome
Feb. 2008 (Broad/cavPor3)
Oct. 2005 (cavPor2) (sequence only)
Hawaiian monk seal
Jun. 2017 (ASM220157v1/neoSch1)
Hedgehog genome
May 2012 (EriEur2.0/eriEur2)
Jun. 2006 (Broad/eriEur1)
Horse genome
Jan. 2018 (EquCab3.0/equCab3)
Sep. 2007 (Broad/equCab2)
Jan. 2007 (Broad/equCab1)
Kangaroo rat genome
Jul. 2008 (Broad/dipOrd1)
Lamprey genome
Dec. 2017 (Pmar_germline 1.0/petMar3)
Sep. 2010 (WUGSC 7.0/petMar2)
Mar. 2007 (WUGSC 3.0/petMar1)
Lancelet genome
Mar. 2006 (JGI 1.0/braFlo1)
Lizard genome
May 2010 (Broad AnoCar2.0/anoCar2)
Jan. 2007 (Broad/anoCar1)
Malayan flying lemur genome
Jun. 2014 (G_variegatus-3.0.2/galVar1)
Manatee genome
Oct. 2011 (Broad v1.0/triMan1)
Marmoset genome
May 2020 (Callithrix_jacchus_cj1700_1.1/calJac4)
Mar. 2009 (WUGSC 3.2/calJac3)
Jun. 2007 (WUGSC 2.0.2/calJac1)
Medaka genome
Oct. 2005 (NIG/UT MEDAKA1/oryLat2)
Medium ground finch genome
Apr. 2012 (GeoFor_1.0/geoFor1)
Megabat genome
Jul. 2008 (Broad/pteVam1)
Microbat genome
Jul. 2010 (Myoluc2.0/myoLuc2)
Minke whale genome
Oct. 2013 (KORDI BalAcu1.0/balAcu1)
Mouse genome
Jun. 2020 (GRCm39/mm39)
Dec. 2011 (GRCm38/mm10)
Jul. 2007 (NCBI37/mm9)
Mar. 2006 (NCBI36/mm8)
Aug. 2005 (NCBI35/mm7)
Mar. 2005 (mm6)
May 2004 (mm5)
Oct. 2003 (mm4)
Feb. 2003 (mm3)
Feb. 2002 (mm2)
Nov. 2001 (mm1)
Mouse lemur genome
May 2015 (Mouse lemur/micMur2)
Jul. 2007 (Broad/micMur1)
Naked mole-rat genome
Jan. 2012 (Broad HetGla_female_1.0/hetGla2)
Jul. 2011 (HetGla_1.0/hetGla1)
Nile tilapia genome
Jan. 2011 (Nile tilapia/oreNil2)
Opossum genome
Oct. 2006 (Broad/monDom5)
Jan. 2006 (Broad/monDom4)
Jun. 2005 (Broad/monDom2)
Oct. 2004 (Broad prelim/monDom1)
Orangutan genome
Jan. 2018 (Susie_PABv2/ponAbe3)
Jul. 2007 (WUGSC 2.0.2/ponAbe2)
Painted turtle genome
Dec. 2011 (v3.0.1/chrPic1)
Panda genome
Dec. 2009 (BGI-Shenzhen 1.0/ailMel1)
Pig genome
Feb. 2017 (SGSC Sscrofa11.1/susScr11)
Aug. 2011 (SGSC Sscrofa10.2/susScr3)
Nov. 2009 (SGSC Sscrofa9.2/susScr2)
Pika genome
May 2012 (OchPri3.0/ochPri3)
Jul. 2008 (Broad/ochPri2)
Platypus genome
Feb. 2007 (ASM227v2/ornAna2)
Mar. 2007 (WUGSC 5.0.1/ornAna1)
Proboscis monkey genome
Nov 2014 (Charlie1.0/nasLar1)
Rabbit genome
Apr. 2009 (Broad/oryCun2)
May 2005 (oryCun1)
Rat genome
Jul. 2014 (RGSC 6.0/rn6)
Mar. 2012 (RGSC 5.0/rn5)
Nov. 2004 (Baylor 3.4/rn4)
Jun. 2003 (Baylor 3.1/rn3)
Jan. 2003 (rn2)
Nov. 2002 (rn1)
Rhesus genome
Feb. 2019 (Mmul_10/rheMac10)
Nov. 2015 (BCM Mmul_8.0.1/rheMac8)
Oct. 2010 (BGI CR_1.0/rheMac3)
Jan. 2006 (MGSC Merged 1.0/rheMac2)
Jan. 2005 (Mmul_0.1/rheMac1)
Rock hyrax genome
Jul. 2008 (Broad/proCap1)
Sheep genome
Nov. 2015 (ISGC Oar_v4.0/oviAri4)
Aug. 2012 (ISGC Oar_v3.1/oviAri3)
Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1)
Shrew genome
Aug. 2008 (Broad/sorAra2)
Jun. 2006 (Broad/sorAra1)
Sloth genome
Jul. 2008 (Broad/choHof1)
Southern sea otter genome
Jun. 2019 (ASM641071v1/enhLutNer1)
Squirrel genome
Nov. 2011 (Broad/speTri2)
Squirrel monkey genome
Oct. 2011 (Broad/saiBol1)
Stickleback genome
Feb. 2006 (Broad/gasAcu1)
Tarsier genome
Sep. 2013 (Tarsius_syrichta-2.0.1/tarSyr2)
Aug. 2008 (Broad/tarSyr1)
Tasmanian devil genome
Feb. 2011 (WTSI Devil_ref v7.0/sarHar1)
Tenrec genome
Nov. 2012 (Broad/echTel2)
Jul. 2005 (Broad/echTel1)
Tetraodon genome
Mar. 2010 (Genoscope 8.0/tetNig2)
Feb. 2004 (Genoscope 7/tetNig1)
Tibetan frog genome
Mar. 2015 (BGI_ZX_2015/nanPar1)
Tree shrew genome
Dec. 2006 (Broad/tupBel1)
Turkey genome
Nov. 2014 (TGC Turkey_5.0/melGal5)
Dec. 2009 (TGC Turkey_2.01/melGal1)
Wallaby genome
Sep. 2009 (TWGS Meug_1.1/macEug2)
White rhinoceros genome
May 2012 (CerSimSim1.0/cerSim1)
X. tropicalis genome
Jul. 2016 (JGI 9.1/xenTro9)
Sep. 2012 (JGI 7.0/xenTro7)
Nov. 2009 (JGI 4.2/xenTro3)
Aug. 2005 (JGI 4.1/xenTro2)
Oct. 2004 (JGI 3.0/xenTro1)
Zebra finch genome
Feb. 2013 (taeGut2/taeGut2)
Jul. 2008 (WUGSC 3.2.4/taeGut1)
Zebrafish genome
May 2017 (GRCz11/danRer11)
Sep. 2014 (GRCz10/danRer10)
Jul. 2010 (Zv9/danRer7)
Dec. 2008 (Zv8/danRer6)
Jul. 2007 (Zv7/danRer5)
Mar. 2006 (Zv6/danRer4)
May 2005 (Zv5/danRer3)
Jun. 2004 (danRer2)
Nov. 2003 (danRer1)
Vertebrates (Sequence only)
The following http://hgdownload.soe.ucsc.edu/gbdb/ location has assembly sequences used in
alignment tracks, such as in the 100-species conservation track. For example, you can find the
underlying mayZeb1.2bit sequence file for the Zebra Mbuna fish assembly, not yet released but used
in the hg38 Vertebrate Multiz Alignment & Conservation (100 Species) track, here:
http://hgdownload.soe.ucsc.edu/gbdb/mayZeb1/. These links also display under a
column titled "UCSC version" on the conservation track description page.
Ciona intestinalis genome
Apr. 2011 (Kyoto KH/ci3)
Mar. 2005 (JGI 2.1/ci2)
Dec. 2002 (JGI 1.0/ci1)
S. purpuratus genome
Sep. 2006 (Baylor 2.1/strPur2)
Apr. 2005 (Baylor 1.1/strPur1)
A. gambiae genome
Nov. 2006 (ICSAGA P3/anoGam3)
Feb. 2003 (IAGEC MOZ2/anoGam1)
A. mellifera genome
May 2005 (Baylor HGSC Amel_3.0/apiMel3)
Jan. 2005 (Baylor 2.0/apiMel2)
Jul. 2004 (Baylor 1.2/apiMel1)
D. ananassae genome
Feb. 2006 (droAna3)
Aug. 2005 (Agencourt prelim/droAna2)
Jul. 2004 (TIGR/droAna1 )
D. erecta genome
Feb. 2006 (droEre2)
Aug. 2005 (Agencourt prelim/droEre1)
D. grimshawi genome
Feb. 2006 (droGri2)
Aug. 2005 (Agencourt prelim/droGri1)
D. melanogaster genome
Aug. 2014 (BDGP Release 6 + ISO1 MT/dm6)
Apr. 2006 (BDGP R5/dm3)
Apr. 2004 (BDGP R4/dm2)
Jan. 2003 (BDGP R3/dm1)
D. mojavensis genome
Feb. 2006 (droMoj3)
Aug. 2005 (Agencourt prelim/droMoj2)
Aug. 2004 (Agencourt prelim/droMoj1)
D. persimilis genome
Oct. 2005 (Broad/droPer1)
D. pseudoobscura genome
Feb. 2006 (dp4)
Nov. 2004 (FlyBase 1.03/dp3)
Aug. 2003 (Baylor freeze1/dp2)
D. sechellia genome
Oct. 2005 (Broad/droSec1)
D. simulans genome
Apr. 2005 (WUGSC mosaic 1.0/droSim1)
D. virilis genome
Feb. 2006 (droVir3)
Aug. 2005 (Agencourt prelim/droVir2)
Jul. 2004 (Agencourt prelim/droVir1)
D. willistoni genome
Feb. 2006 (droWil1)
D. yakuba genome
Nov. 2005 (WUGSC 7.1/droYak2)
Apr. 2004 (WUGSC 1.0/droYak1)
T. castaneum genome
Sep. 2005 (triCas2)
C. brenneri genome
Feb. 2008 (WUGSC 6.0.1/caePb2)
Jan. 2007 (WUGSC 4.0/caePb1)
C. briggsae genome
Jan. 2007 (WUGSC 1.0/cb3)
Jul. 2002 (cb1)
C. elegans genome
Feb. 2013 (WBcel235/ce11)
Oct. 2010 (WS220/ce10)
May 2008 (WS190/ce6)
Jan. 2007 (WS170/ce4)
Mar. 2004 (WS120/ce2)
May 2003 (ce1)
C. japonica genome
Mar. 2008 (WUGSC 3.0.2/caeJap1)
C. remanei genome
May 2007 (WUGSC 15.0.1/caeRem3)
Mar. 2006 (WUGSC 1.0/caeRem2)
P. pacificus genome
Feb. 2007 (WUGSC 5.0/priPac1)
Yeast (S. cerevisiae) genome
Apr. 2011 (SacCer_Apr2011/sacCer3)
Jun. 2008 (SGD/sacCer2)
Oct. 2003 (SGD/sacCer1)
Sea Hare genome
Sep. 2008 (Broad 2.0/aplCal1)
Denisova genome
Ebola virus genome
Jun. 2014 (G3683/KM034562.1/eboVir3)
SARS-CoV-2 genome
Jan. 2020 (ASM985889v3/wuhCor1)
Data access through the gbdb fileserver
The /gbdb fileserver offers access to all files referenced by the Genome Browser tables with servers
in North America and
Europe. Some files in the
browser, such as bigBed files, are hosted in binary format. For example, in the hg38 database, the
crispr.bb and crisprDetails.tab files for the
CRISPR track
can be found using the following URLs:
Individual regions or the whole genome annotation from such binary files can be obtained using tools
such as bigBedToBed
, which can be compiled from the source code or downloaded as a
precompiled binary for your system (see the Source and utilities
downloads section). The bigBedToBed
tool can also be used to obtain a
specific subset of features within a given range, e.g.:
bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/crispr/crispr.bb -chrom=chr21 -start=25000000 -end=30000000 stdout
bigBedToBed http://hgdownload-euro.soe.ucsc.edu/gbdb/hg38/crispr/crispr.bb -chrom=chr21 -start=25000000 -end=30000000 stdout
Sequence files for assemblies used in alignment tracks, such as in the 100-species Conservation
track, are also found on the /gbdb server. For example, you can find the underlying
mayZeb1.2bit sequence file for the Zebra Mbuna fish assembly, which is used in the
hg38 Vertebrate Multiz
Alignment and Conservation (100 Species) track, but is not available as a standalone browser:
Data on the gbdb fileserver can also be acquired using the rsync
commands outline
on our
FTP downloads page.
This technique is especially useful for downloading large files.
Data Access using the JSON API
The JSON API can also be used to query and download gbdb data in JSON format. Below are two examples
of how to query and download gbdb data using the JSON API, respectively.
http://api.genome.ucsc.edu/getData/track?genome=hg38;track=ncbiRefSeqOther;chrom=chr21;start=25000000;end=30000000
wget -O- 'http://api.genome.ucsc.edu/getData/track?genome=hg38;track=ncbiRefSeqOther;chrom=chr21;start=25000000;end=30000000' > out.json
For more information see the
JSON API help page.
Data shared by multiple assemblies
LiftOver files (over.chain)
The links to liftOver over.chain files can be found in the corresponding assembly sections
above. For example, the link for the mm5-to-mm6 over.chain file is located in the mm5
downloads section. The link to download the liftOver source is located in the
Source and utilities downloads section.