Sequence and Annotation Downloads

This page contains links to sequence and annotation data downloads for the genome assemblies featured in the UCSC Genome Browser. Table downloads are also available via the Genome Browser FTP server. For quick access to the most recent assembly of each genome, see the current genomes directory. This directory may be useful to individuals with automated scripts that must always reference the most recent assembly. To query and download data in JSON format, use our JSON API.

To view the current descriptions and formats of the tables in the annotation database, use the "describe table schema" button in the Table Browser.

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

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:

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)

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)

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

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)

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

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.