Vertebrate Genomes assembly hubs

Assemblies from NCBI/Genbank/Refseq sources, subset of other vertebrates only.

How to view the hub

Options:

  1. The links to the genome browser in the table below will attach that one specific assembly to the genome browser. This is most likely what you want. Alternatively, the entire set of assemblies can be attached as one group to the genome browser with the following links depending upon which of our mirror site browsers you prefer to use:
    attach all assemblies to selected site:   genome.ucsc.edu   genome-euro.ucsc.edu   genome-asia.ucsc.edu
  2. To manually attach all the assemblies in this hub to genome browsers that are not one of the three UCSC mirror sites:
    1. From the blue navigation bar, go to My Data -> Track Hubs
    2. Then select the My Hubs tab and enter this URL into the textbox:
      https://hgdownload.soe.ucsc.edu/hubs/vertebrate/hub.txt
    3. Once you have added the URL to the entry form, press the Add Hub button to add the hub.

After adding the hub, you will be redirected to the gateway page. The genome assemblies can be selected from the Vertebrate Hub Assembly dropdown menu. Instead of adding all the assemblies in one collected group, use the individual view in browser in the table below.

See also: assembly statisticstrack statistics <== additional information for these assemblies.


Data resource links

NOTE: Click on the column headers to sort the table by that column

The common name and view in browser will attach only that single assembly to the genome browser.
The scientific name and data download link provides access to the files for that one assembly hub.
The other links provide access to NCBI resources for these assemblies.
count common name and
view in browser
scientific name
and data download
NCBI assembly BioSample BioProject assembly date,
source link
1 Abingdon island giant tortoise Chelonoidis abingdonii GCF_003597395.1_ASM359739v1 SAMN07840320 PRJNA416050 2018-09-25
2 African clawed frog (2021) Xenopus laevis GCF_017654675.1_Xenopus_laevis_v10.1 SAMN18035302 PRJNA313213 2021-04-12
3 American alligator Alligator mississippiensis GCF_000281125.3_ASM28112v4 SAMN02981418 PRJNA159843 2016-03-28
4 Asiatic toad (SCDJY-AF-19 2020) Bufo gargarizans GCF_014858855.1_ASM1485885v1 SAMN14734018 PRJNA628553 2020-10-21
5 Australian saltwater crocodile Crocodylus porosus GCF_001723895.1_CroPor_comp1 SAMN03102602 PRJNA163131 2016-09-13
6 brown spotted pit viper Protobothrops mucrosquamatus GCF_001527695.2_P.Mucros_1.0 SAMD00043515 PRJDB4386 2016-01-22
7 Burmese python Python bivittatus GCF_000186305.1_Python_molurus_bivittatus-5.0.2 SAMN02981298 PRJNA61243 2013-09-15
8 central bearded dragon Pogona vitticeps GCF_900067755.1_pvi1.1 SAMEA2300447 PRJEB5206 2017-02-28
9 Chinese alligator Alligator sinensis GCF_000455745.1_ASM45574v1 SAMN02981559 PRJNA215016 2013-08-29
10 Chinese soft-shelled turtle Pelodiscus sinensis GCF_000230535.1_PelSin_1.0 SAMN02981371 PRJNA68233 2012-07-24
11 coelacanth Latimeria chalumnae GCF_000225785.1_LatCha1 SAMN00138723 PRJNA56111 2011-09-12
12 common garter snake Thamnophis sirtalis GCF_001077635.1_Thamnophis_sirtalis-6.0 SAMN03759628 PRJNA189551 2015-06-26
13 common wall lizard Podarcis muralis GCF_004329235.1_PodMur_1.0 SAMN10820182 PRJNA515813 2019-03-07
14 common toad Bufo bufo GCF_905171765.1_aBufBuf1.1 SAMEA7521636 PRJEB42168 2021-01-28
15 corn snake Pantherophis guttatus GCF_001185365.1_UNIGE_PanGut_3.0 SAMN12106767 PRJNA268069 2020-04-13
16 eastern brown snake Pseudonaja textilis GCF_900518735.1_EBS10Xv2-PRI SAMEA4800208 PRJEB27869 2018-09-24
17 elephant shark (2021) Callorhinchus milii GCF_018977255.1_IMCB_Cmil_1.0 SAMN12905446 PRJNA575613 2021-06-21
18 epaulette shark (sHemOce1 2021 VGP) Hemiscyllium ocellatum GCA_020745735.1_sHemOce1.pat.X.cur. SAMN22550098 PRJNA774310 2021-11-05
19 epaulette shark (alt pseudohaplotype sHemOce1 2021 VGP) Hemiscyllium ocellatum GCA_020745765.1_sHemOce1.mat.decon SAMN22550098 PRJNA774309 2021-11-05
20 European common frog Rana temporaria GCF_905171775.1_aRanTem1.1 SAMEA7521635 PRJEB42171 2021-01-28
21 European eel Anguilla anguilla GCF_013347855.1_fAngAng1.pri SAMN12623627 PRJNA561979 2020-06-18
22 fence lizard Sceloporus undulatus GCF_019175285.1_SceUnd_v1.1 SAMN14373011 PRJNA612440 2021-07-08
23 Gaboon caecilian (alt pseudohaplotype 2019 VGP) Geotrypetes seraphini GCA_902459495.1_aGeoSer1.1_alternate_haplotype SAMEA104387963 PRJEB33991 2019-08-18
24 Gaboon caecilian (2019 refseq VGP) Geotrypetes seraphini GCF_902459505.1_aGeoSer1.1 SAMEA104387963 PRJEB33992 2019-08-18
25 gharial Gavialis gangeticus GCF_001723915.1_GavGan_comp1 SAMN03102901 PRJNA172383 2016-09-13
26 Goodes thornscrub tortoise (Sinaloan 2019 VGP) Gopherus evgoodei GCF_007399415.2_rGopEvg1_v1.p SAMN03496275 PRJNA489103 2019-07-25
27 Goodes thornscrub tortoise (Sinaloan alt pseudohaplotype 2019 VGP) Gopherus evgoodei GCA_007399395.1_rGopEvg1_v1.alt SAMN03496275 PRJNA489104 2019-07-24
28 gray bichir Polypterus senegalus GCF_016835505.1_ASM1683550v1 SAMN13737739 PRJNA599026 2021-02-09
29 great white shark Carcharodon carcharias GCF_017639515.1_sCarCar2.pri SAMN12629504 PRJNA562007 2021-03-30
30 green anole Anolis carolinensis GCF_000090745.1_AnoCar2.0 SAMN02981230 PRJNA18787 2011-01-10
31 green sea turtle (v2 2021) Chelonia mydas GCF_015237465.2_rCheMyd1.pri.v2 SAMN12612360 PRJNA561941 2021-07-15
32 High Himalaya frog Nanorana parkeri GCF_000935625.1_ASM93562v1 SAMN02720813 PRJNA243398 2015-03-17
33 Komodo dragon (SLA01 2019) Varanus komodoensis GCF_004798865.1_ASM479886v1 SAMN10967258 PRJNA523222 2019-04-17
34 Lataste's viper (rVipLat1 2022 VGP) Vipera latastei GCA_024294585.1_rVipLat1.pri SAMN28408464 PRJNA838200 2022-07-20
35 leatherback sea turtle (v4 2021 refseq G10K VGP) Dermochelys coriacea GCF_009764565.3_rDerCor1.pri.v4 SAMN12629498 PRJNA561993 2021-08-25
36 leatherback sea turtle (alt pseudohaplotype 2019 VGP) Dermochelys coriacea GCA_009762595.1_rDerCor1.alt SAMN12629498 PRJNA561994 2019-12-18
37 loggerhead turtle (SJ_126:Eziel1 2022) Caretta caretta GCF_023653815.1_GSC_CCare_1.0 SAMN27958248 PRJNA826225 2022-06-07
38 mainland tiger snake Notechis scutatus GCF_900518725.1_TS10Xv2-PRI SAMEA4800209 PRJEB27871 2018-09-24
39 marbled whiptail (SIMRID8450 2020) Aspidoscelis marmoratus GCA_014337955.1_AspMar1.0 SAMN06204250 PRJNA360150 2020-08-31
40 meadow viper (2022 VGP) Vipera ursinii GCA_947247035.1_rVipUrs1.1 SAMEA12832258 PRJEB57183 2022-10-30
41 Mexican gopher tortoise (WGS:JAMKFC01 2022 VGP) Gopherus flavomarginatus GCF_025201925.1_rGopFla2.mat.asm SAMN24199108 PRJNA794188 2022-09-15
42 Mexican gopher tortoise (WGS:JAMKFD01 2022 VGP) Gopherus flavomarginatus GCA_025201965.1_rGopFla2.pat.asm SAMN24199108 PRJNA794189 2022-09-08
43 Mississippi paddlefish Polyodon spathula GCF_017654505.1_ASM1765450v1 SAMN09842169 PRJNA484687 2021-03-31
44 red-eared slider turtle Trachemys scripta elegans GCF_013100865.1_CAS_Tse_1.0 SAMN12189062 PRJNA552319 2020-05-15
45 reedfish Erpetoichthys calabaricus GCF_900747795.1_fErpCal1.1 SAMEA104026374 PRJEB31579 2019-03-26
46 Reeves's turtle Mauremys reevesii GCF_016161935.1_ASM1616193v1 SAMN16454374 PRJNA663192 2020-12-22
47 sand lizard (alt pseudohaplotype 2019 VGP) Lacerta agilis GCA_009819545.1_rLacAgi1.alt SAMN12629509 PRJNA562019 2019-12-23
48 sand lizard (2019 VGP) Lacerta agilis GCF_009819535.1_rLacAgi1.pri SAMN12629509 PRJNA562018 2019-12-31
49 Schlegel's Japanese gecko Gekko japonicus GCF_001447785.1_Gekko_japonicus_V1.1 SAMN04157958 PRJNA298277 2015-11-25
50 sea lamprey (alt pseudohaplotype 2020 VGP) Petromyzon marinus GCA_010993595.1_kPetMar1.alt SAMN12629506 PRJNA562012 2020-02-24
51 sea lamprey (2020 VGP) Petromyzon marinus GCF_010993605.1_kPetMar1.pri SAMN12629506 PRJNA562011 2020-02-24
52 smaller spotted catshark Scyliorhinus canicula GCF_902713615.1_sScyCan1.1 SAMEA994730 PRJEB35945 2020-12-17
53 smalltooth sawfish (2019 VGP) Pristis pectinata GCA_009764475.1_sPriPec2.pri SAMN12629505 PRJNA562009 2019-12-19
54 smalltooth sawfish (alt pseudohaplotype 2019 VGP) Pristis pectinata GCA_009764485.1_sPriPec2.alt SAMN12629505 PRJNA562010 2019-12-18
55 spotted gar Lepisosteus oculatus GCF_000242695.1_LepOcu1 SAMN00706774 PRJNA68247 2012-01-13
56 sterlet Acipenser ruthenus GCF_010645085.1_ASM1064508v1 SAMN12612932 PRJNA561280 2020-02-19
57 thorny skate (CabotCenter1 v1.1 2020 VGP) Amblyraja radiata GCF_010909765.2_sAmbRad1.1.pri SAMN09948523 PRJNA591369 2020-02-21
58 thorny skate (alt pseudohaplotype CabotCenter1 2020 VGP) Amblyraja radiata GCA_010909745.1_sAmbRad1.alt SAMN09948523 PRJNA591368 2020-02-14
59 three-toed box turtle Terrapene carolina triunguis GCF_002925995.2_T_m_triunguis-2.0 SAMN08285364 PRJNA415469 2018-09-21
60 tiger rattlesnake Crotalus tigris GCF_016545835.1_ASM1654583v1 SAMN12497667 PRJNA558767 2021-01-06
61 tiny Cayenne caecilian Microcaecilia unicolor GCF_901765095.1_aMicUni1.1 SAMEA104387962 PRJEB32737 2019-06-22
62 tiny Cayenne caecilian (alt pseudohaplotype 2019 VGP) Microcaecilia unicolor GCA_901765105.1_aMicUni1.1_alternate_haplotype SAMEA104387962 PRJEB32738 2019-07-08
63 Townsend's dwarf sphaero (gecko TG3544 2022) Sphaerodactylus townsendi GCF_021028975.2_MPM_Stown_v2.3 SAMN20179316 PRJNA746057 2022-04-08
64 tropical clawed frog Xenopus tropicalis GCF_000004195.4_UCB_Xtro_10.0 SAMN13041969 PRJNA577946 2019-11-14
65 two-lined caecilian (2019 VGP) Rhinatrema bivittatum GCF_901001135.1_aRhiBiv1.1 SAMEA104387956 PRJEB32111 2019-06-02
66 two-lined caecilian (alt pseudohaplotype 2019 VGP) Rhinatrema bivittatum GCA_901001175.1_aRhiBiv1.1_alternate_haplotype SAMEA104387956 PRJEB32112 2019-06-02
67 viviparous/common lizard Zootoca vivipara GCF_011800845.1_UG_Zviv_1 SAMN14329711 PRJNA610958 2020-04-01
68 West African lungfish Protopterus annectens GCF_019279795.1_PAN1.0 SAMN17890435 PRJNA701604 2021-07-20
69 western painted turtle (v304 2020) Chrysemys picta bellii GCF_000241765.4_Chrysemys_picta_BioNano-3.0.4 SAMN02713681 PRJNA78657 2020-08-21
70 western terrestrial garter snake (alt pseudohaplotype 2019 VGP) Thamnophis elegans GCA_009769695.1_rThaEle1.alt SAMN12629499 PRJNA561997 2019-12-19
71 western terrestrial garter snake (2019 VGP) Thamnophis elegans GCF_009769535.1_rThaEle1.pri SAMN12629499 PRJNA561996 2019-12-23
72 whale shark (Ralph 2017 Emory U) Rhincodon typus GCF_001642345.1_ASM164234v2 SAMN04562461 PRJNA255419 2017-03-03
73 whale shark (14 2022 Squalomix) Rhincodon typus GCF_021869965.1_sRhiTyp1.1 SAMN19519256 PRJNA703743 2022-02-03
74 whitespotted bambooshark Chiloscyllium plagiosum GCF_004010195.1_ASM401019v2 SAMN09508879 PRJNA478295 2019-01-10
75 yellowpond turtle (Southern MM-2020 2021) Mauremys mutica GCF_020497125.1_ASM2049712v1 SAMN19136605 PRJNA729638 2021-10-14
76 zebra shark (6-17 2022 Squalomix) Stegostoma fasciatum GCF_022316705.1_sSteFas1.1 SAMN18022887 PRJNA703743 2022-02-17

Additional hubs with collections of assemblies
Collection Hub index pages: Assembly statistics: Track statistics:
Primates 59 assemblies assembly stats track stats
Mammals 357 assemblies assembly stats track stats
Birds 175 assemblies assembly stats track stats
Fishes 195 assemblies assembly stats track stats
other vertebrates 76 assemblies assembly stats track stats
Invertebrates 470 assemblies assembly stats track stats
Plants 173 assemblies assembly stats track stats
Fungi 463 assemblies assembly stats track stats
Viruses 254 assemblies assembly stats track stats
Bacteria 14 assemblies assembly stats track stats
VGP - Vertebrate Genome Project 261 assemblies assembly stats track stats
legacy/superseded 242 assemblies assembly stats track stats