hgdownload.soe.ucsc.edu

UCSC Genome Browser 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 our JSON API, MySQL server, or FTP server. Data filtering is available in the Table Browser or via the command-line utilities.

For access to the most recent assembly of each genome, see the current genomes directory. Previous versions of certain data are available from our track archive. Data hosted in Public Hubs exists on external sites. GenArk (Genome Archive) species data can be found here. All data in the Genome Browser are freely usable for any purpose except as indicated in the README.txt files in the download directories. 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.

Jan. 2022 (T2T-CHM13 v2.0/hs1)

This assembly represents the T2T-CHM13v2.0 genome. While it may be more recent than hg38, hg38 is still the latest GRCh assembly and is better annotated by most projects.

This assembly is served entirely as a track hub, meaning no MySQL files exist.

Dec. 2013 (GRCh38/hg38)

Feb. 2009 (GRCh37/hg19)

Mar. 2006 (NCBI36/hg18)

May 2004 (NCBI35/hg17)

Jul. 2003 (NCBI34/hg16)

Apr. 10, 2003 (hg15)

Nov. 14, 2002 (hg13)

Jun. 28, 2002 (hg12)

Apr. 5, 2002 (hg11)

Dec. 22, 2001 (hg10)

Aug. 6, 2001 (hg8)

Apr. 1, 2001 (hg7)

Dec. 12, 2000 (hg6)

Oct. 7, 2000 (hg5)

Oct. 7, 2000 preliminary version

Sep. 5, 2000 (hg4)

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)

Ciona intestinalis genome

Apr. 2011 (Kyoto KH/ci3)

Mar. 2005 (JGI 2.1/ci2)

Dec. 2002 (JGI 1.0/ci1)

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

Oct. 2020 (Dog10K_Boxer_Tasha/canFam6)

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)

Fruit fly genomes

Aug. 2014 (BDGP Release 6 + ISO1 MT/dm6)

Apr. 2006 (BDGP R5/dm3)

Apr. 2004 (BDGP R4/dm2)

Jan. 2003 (BDGP R3/dm1)

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 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

Nov. 2020 (mRatBN7.2/rn7)

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

Nov. 2019 (UCB_Xtro_10.0/xenTro10)

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)

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. 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)

May 2022 (MT903340.1/mpxvRivers)

Zebrafish genomes

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)

Sequence only Downloads

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.

Utility Tools and Software downloads

The source code for the Genome Browser, Blat, liftOver and other utilities is free for non-profit academic research and personal use. For information on commercial licensing, see the Genome Browser license and Blat license requirements. The source and executables for several of these products can be downloaded or purchased from our online store.

Mirroring the Genome Browser

You can install a local mirrored copy of the Genome Browser website on your web server, eliminating the need to compile the entire source tree and providing customization and privacy options.

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 (file format converters, data query tools, etc.)

    • Run programs without arguments to see an instructional usage message. All our command-line tools can be obtained as ready-to-use binaries from our download server for the respective operating system. To download all command line utilities into a directory with the correct permission bits set, use the following command:
    $ rsync -aP hgdownload.soe.ucsc.edu::genome/admin/exe/linux.x86_64/ ./
    Note about 'permission denied' error when downloading with https, curl, or wget:
    In order for your computer to run a freshly downloaded utility, you will need to change the file permissions to allow your operating system to run the program. To make utilities usable, download a tool and turn on its 'executable' bit: 
    $ wget https://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/liftOver
$ 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 build and 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.

Data access through the gbdb server

The /gbdb fileserver offers access to all files referenced by the Genome Browser tables, with servers in North America and Europe for faster downloads. Many 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 whole genome annotations from binary files can be obtained using tools such as bigBedToBed, which can be 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

Data Access to GenArk Hub genomes

The GenArk Hubs allow visualization of thousands of NCBI genomes previously not available on the Genome Browser. The underlying data can be accessed by clicking the clade (e.g. primates) finding your organism or assembly, and clicking the download link in the third column. For direct link to a particular GCA or GCF assembly ID, you can model your links after this example, where IDs are separated by slashes each three characters.

You can find more examples of downloading GenArk data in our FAQ section.

Data Access through the Public MySql Server

UCSC Genome Browser supports a public MySql server with annotation data available for filter and query. For more information on this service, see our MySQL server page.

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 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