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  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 view the current descriptions and formats of the tables in the annotation database, use the "describe table schema" button in the Table Browser. The Description of the annotation database page (no longer maintained) also provides descriptions of selected tables in the database.

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.

VERTEBRATES - Complete annotation sets
  Human
  Alpaca
  American alligator
  Armadillo
  Atlantic cod
  Baboon
  Bonobo
  Brown kiwi
  Budgerigar
  Bushbaby
  Cat
  Chicken
  Chimpanzee
  Chinese hamster
  Coelacanth
  Cow
  Crab-eating macaque
  Dog
  Dolphin
  Elephant
  Elephant shark
  Ferret
  Fugu
  Gibbon
  Gorilla
Green Monkey
Guinea pig
Hedgehog
Horse
Kangaroo rat
Lamprey
Lizard
Malayan flying lemur
Manatee
Marmoset
Medaka
Medium ground finch
Megabat
Microbat
Minke whale
Mouse
Mouse lemur
Naked mole-rat
Nile tilapia
Opossum
Orangutan
Painted turtle
Panda
Pig
Pika
Platypus
Rabbit
Rat
Rhesus
Rock hyrax
Sheep
Shrew
Sloth
Squirrel
Squirrel monkey
Stickleback
Tarsier
Tasmanian devil
Tenrec
Tetraodon
Tree shrew
Turkey
Wallaby
White rhinoceros
X. tropicalis
Zebra finch
Zebrafish
 

VERTEBRATES - Sequence downloads only
  Armadillo
  Bushbaby
  J. Craig Venter
  Data access for non-browser assemblies

DEUTEROSTOMES
  C. intestinalis
  Lancelet
  S. purpuratus

INSECTS
  A. gambiae   D. pseudoobscura
  A. mellifera   D. sechellia
  D. ananassae   D. simulans
  D. erecta   D. virilis
  D. grimshawi   D. willistoni
  D. melanogaster   D. yakuba
  D. mojavensis   T. castaneum
  D. persimilis   

NEMATODES
  C. brenneri
  C. briggsae
  C. elegans
  C. japonica
  C. remanei
  P. pacificus

YEAST AND OTHERS
  S. cerevisiae
  Sea hare
  Denisova

VIRUSES
  Ebola virus

OTHER DOWNLOADS
  Access the gbdb Fileserver
  Shared Data (Protein DBs, hgFixed, visiGene)
  LiftOver Files
  ENCODE Project Files (Genome-wide Phase)
  ENCODE Project Files (Pilot Phase)


  Source & Utilities Downloads
 

The Genome Browser, Blat, and liftOver source are freely downloadable for academic, noncommercial, and personal use. For information on commercial licensing, please see the Genome Browser and Blat licensing requirements.

Genome Browser Mirror
The Genome Browser Mirror is available for installing a local copy of the Genome Browser website onto your web server. We provide precompiled executable binaries for this purpose, so you do not have to compile the whole source code.

Troubleshooting: For slow download speeds, try using UDR (UDT Enabled Rsync), which improves throughput of large data transfers over long distances (64/32-bit also available).

Utilities
Please review the userApps README for a summary of how to fetch selected directories from the kent source tree, or download userApps.src.tgz, to install all kent utilities.

The utilities directory offers downloads of pre-compiled standalone binaries:

Online Store
The following can be downloaded from our online store:

  • Genome Browser Source Code
  • Genome Browser in a Box (GBiB)
  • LiftOver Program

  Human Genome
 

Dec. 2013 (GRCh38/hg38)

Feb. 2009 (GRCh37/hg19)

Mar. 2006 (NCBI36/hg18)

May 2004 (NCBI35/hg17)

July 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):

June 15, 2000:

May 24, 2000:

Older Human data and documentation:


  Alpaca Genome
 

Mar. 2013 (Vicugna_pacos-2.0.1/vicPac2)

July 2008 (Broad/vicPac1)

  American alligator Genome
 

August 2012 (allMis0.2/allMis1)

  Armadillo Genome
 

Dec. 2011 (Baylor/dasNov3)

  Atlantic cod Genome
 

May 2010 (Genofisk GadMor_May2010/gadMor1)

  Baboon Genome
 

Mar. 2012 (Baylor Panu_2.0/papAnu2)

Nov. 2008 (Baylor Pham_1.0/papHam1)

  Bonobo Genome
 

May 2012 (Max-Planck/panPan1)

  Brown Kiwi Genome
 

June 2015 (MPI-EVA AptMant0/aptMan1)

  Budgerigar Genome
 

Sep. 2011 (WUSTL v6.3/melUnd1)

  Bushbaby Genome
 

Mar. 2011 (Broad/otoGar3)

  Cat Genome
 

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
 

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
 

May. 2016 (Pan_tro 3.0/panTro5)

Feb. 2011 (CSAC 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
 

Jul. 2013 (C_griseus_v1.0/criGri1)

  Coelacanth Genome
 

Aug. 2011 (LatCha1/latCha1)

  Cow Genome
 

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)/bosTau5)

Oct. 2007 (Baylor 4.0/bosTau4)

Aug. 2009 (bosTauMd3)/bosTauMd3)

Aug. 2006 (Baylor 3.1/bosTau3)

Mar. 2005 (Baylor 2.0/bosTau2)

May 2004 (bosTau1/bosTau1)


  Crab-eating macaque Genome
 

Jun. 2013 (Macaca_fascicularis_5.0/macFas5)

  Dog Genome
  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
 

April 2011 (MusPutFur1.0/musFur1)

  Fugu Genome
 

Oct. 2011 (FUGU5/fr3/fr3)

Oct. 2004 (JGI V4.0/fr2)

Aug. 2002 (fugu/fr1)


  Gibbon Genome
 

Oct. 2012 (Nleu_3.0/nomLeu3)

June 2011 (GGSC Nleu1.1/nomLeu2)

Jan. 2010 (GGSC Nleu1.0/nomLeu1)

  Gorilla Genome
 

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)

June 2006 (Broad/eriEur1)

  Horse Genome
 

Sep. 2007 (Broad/equCab2)

Jan. 2007 (Broad/equCab1)


  Kangaroo rat Genome
 

July 2008 (Broad/dipOrd1)

  Lamprey Genome
 

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
 

June 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
 

July 2008 (Broad/pteVam1)

  Microbat Genome
 

Jul. 2010 (Myoluc2.0/myoLuc2)


  Minke whale Genome
 

Oct. 2013 (KORDI BalAcu1.0/balAcu1)


  Mouse Genome
 

Dec. 2011 (GRCm38/mm10)

Jul. 2007 (NCBI37/mm9)

Mar. 2006 (NCBI36/mm8)

Aug. 2005 (NCBI35/mm7)

Mar. 2005 (mm6/mm6)

May 2004 (mm5/mm5)

Oct. 2003 (mm4/mm4)

Feb. 2003 (mm3/mm3)

Feb. 2002 (mm2/mm2)

Nov. 2001 (mm1/mm1)


  Mouse lemur Genome
 

May 2015 (Mouse lemur/micMur2)

July 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)

  • Multiple Alignments

    Jan. 2006 (Broad/monDom4)

    Jun. 2005 (Broad/monDom2)

    Oct. 2004 (Broad prelim/monDom1)


  •   Orangutan Genome
     

    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
     

    Aug. 2011 (SGSC Sscrofa10.2/susScr3)

    Nov. 2009 (SGSC Sscrofa9.2/susScr2)


      Pika Genome
     

    May 2012 (OchPri3.0/ochPri3)

    July 2008 (Broad/ochPri2)

      Platypus Genome
     

    Feb. 2007 (ASM227v2/ornAna2)

    Mar. 2007 (WUGSC 5.0.1/ornAna1)


      Rabbit Genome
     

    Apr. 2009 (Broad/oryCun2)

    May 2005 (oryCun1/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/rn2)

    Nov. 2002 (rn1/rn1)


      Rhesus Genome
     

    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
     

    July 2008 (Broad/proCap1)

      Sheep Genome
     

    Aug. 2012 (ISGC Oar_v3.1/oviAri3)

    Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1)


      Shrew Genome
     

    Aug. 2008 ((Broad/sorAra2)

    June 2006 (Broad/sorAra1)

      Sloth Genome
     

    July 2008 (Broad/choHof1)

      Squirrel Genome
     

    Nov. 2011 (Broad/speTri2)

      Squirrel monkey Genome
     

    Oct. 2011 (Broad/saiBol1)

      Stickleback Genome
     

    Feb. 2006 (Broad/gasAcu1)

  • Multiple Alignments

  •   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)

    July 2005 (Broad/echTel1)

      Tetraodon Genome
     

    Mar. 2010 (Genoscope 8.0/tetNig2)

    Feb. 2004 (Genoscope 7/tetNig1)


      Tree shrew Genome
     

    Dec. 2006 (Broad/tupBel1)

      Turkey Genome
     

    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
     

    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
     

    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/danRer2)

    Nov. 2003 (danRer1/danRer1)


      Vertebrates (sequence only)
     


      C. intestinalis Genome
     

    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
     

    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/droAna3)

    Aug. 2005 (Agencourt prelim/droAna2)

    Jul. 2004 (TIGR/droAna1 )


      D. erecta Genome
     

    Feb. 2006 (droEre2/droEre2)

    Aug. 2005 (Agencourt prelim/droEre1)


      D. grimshawi Genome
     

    Feb. 2006 (droGri2/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)

    July 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)

    July 2002 (WormBase cb25.agp8/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)

    June 2008 (SGD/sacCer2)

    Oct. 2003 (SGD/sacCer1)


      Sea Hare (Aplysia californica) Genome
     

    Sept. 2008 (Broad 2.0/aplCal1)


      Denisova Genome
     


      Ebola Virus Genome
     

    June 2014 (G3683/KM034562.1/eboVir3)

      Data Access through the gbdb Fileserver
     

    • The /gbdb fileserver holds all files referenced by the genome browser tables. Some files in the browser are hosted in binary files such as a bigBed file that can be downloaded from our download server from the /gbdb location.
      • Examples for the hg38 database are the crispr.bb and crisprDetails.tab files for the CRISPR track which can be found here.
      • Individual regions or the whole genome annotation from such binary files can be obtained using tools like bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here.
      • The bigBedToBed tool can also be used to obtain only features within a given range,
        e.g. bigBedToBed http://hgdownload.cse.ucsc.edu/gbdb/hg38/crispr/crispr.bb -chrom=chr21 -start=25000000 -end=30000000 stdout

    • Sequence files for assembly sequences used in alignment tracks, such as in the 100-species conservation track are also found in the /gbdb location.

      Data Shared by Multiple Assemblies
     

      LiftOver Files (over.chain)
     

    The liftOver links have been moved to the corresponding assembly sections (for example, the link for the mm5-to-mm6 over.chain file is now located in the mm5 downloads section). The liftOver source download link is now located in the source downloads section.