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 statistics, track 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 Aeolian wall lizard (rPodRaf1 primary hap 2022) Podarcis raffonei GCF_027172205.1_rPodRaf1.pri SAMN28455423 PRJNA839511 2022-12-27
3 African clawed frog (2021) Xenopus laevis GCF_017654675.1_Xenopus_laevis_v10.1 SAMN18035302 PRJNA313213 2021-04-12
4 American alligator Alligator mississippiensis GCF_000281125.3_ASM28112v4 SAMN02981418 PRJNA159843 2016-03-28
5 Asiatic toad (SCDJY-AF-19 2020) Bufo gargarizans GCF_014858855.1_ASM1485885v1 SAMN14734018 PRJNA628553 2020-10-21
6 Australian saltwater crocodile Crocodylus porosus GCF_001723895.1_CroPor_comp1 SAMN03102602 PRJNA163131 2016-09-13
7 Blainville's horned lizard (primary hap 2022) Phrynosoma blainvillii GCA_026167985.1_rPhrBla1.0.hap1 SAMN29046554 PRJNA873122 2022-11-14
8 Blainville's horned lizard (alternate hap 2022) Phrynosoma blainvillii GCA_026167975.1_rPhrBla1.0.hap2 SAMN29046554 PRJNA873121 2022-11-14
9 brown spotted pit viper Protobothrops mucrosquamatus GCF_001527695.2_P.Mucros_1.0 SAMD00043515 PRJDB4386 2016-01-22
10 Burmese python Python bivittatus GCF_000186305.1_Python_molurus_bivittatus-5.0.2 SAMN02981298 PRJNA61243 2013-09-15
11 California glossy snake (A.elegans occidentalis HBS 135684 alternate hap 2022) Arizona elegans GCA_022578425.1_rAriEle1.0.a SAMN24818160 PRJNA796780 2022-03-15
12 California glossy snake (A.elegans occidentalis HBS 135684 primary hap 2022) Arizona elegans GCA_022577455.1_rAriEle1.0.p SAMN24818160 PRJNA796781 2022-03-15
13 central bearded dragon Pogona vitticeps GCF_900067755.1_pvi1.1 SAMEA2300447 PRJEB5206 2017-02-28
14 Chinese alligator Alligator sinensis GCF_000455745.1_ASM45574v1 SAMN02981559 PRJNA215016 2013-08-29
15 Chinese soft-shelled turtle Pelodiscus sinensis GCF_000230535.1_PelSin_1.0 SAMN02981371 PRJNA68233 2012-07-24
16 coelacanth Latimeria chalumnae GCF_000225785.1_LatCha1 SAMN00138723 PRJNA56111 2011-09-12
17 common garter snake Thamnophis sirtalis GCF_001077635.1_Thamnophis_sirtalis-6.0 SAMN03759628 PRJNA189551 2015-06-26
18 common wall lizard Podarcis muralis GCF_004329235.1_PodMur_1.0 SAMN10820182 PRJNA515813 2019-03-07
19 common toad Bufo bufo GCF_905171765.1_aBufBuf1.1 SAMEA7521636 PRJEB42168 2021-01-28
20 corn snake Pantherophis guttatus GCF_001185365.1_UNIGE_PanGut_3.0 SAMN12106767 PRJNA268069 2020-04-13
21 diamondback terrapin (rMalTer1 2023) Malaclemys terrapin pileata GCF_027887155.1_rMalTer1.hap1 SAMN31394215 PRJNA895896 2023-01-18
22 eastern brown snake Pseudonaja textilis GCF_900518735.1_EBS10Xv2-PRI SAMEA4800208 PRJEB27869 2018-09-24
23 elephant shark (2021) Callorhinchus milii GCF_018977255.1_IMCB_Cmil_1.0 SAMN12905446 PRJNA575613 2021-06-21
24 epaulette shark (sHemOce1 2021) Hemiscyllium ocellatum GCA_020745735.1_sHemOce1.pat.X.cur. SAMN22550098 PRJNA774310 2021-11-05
25 epaulette shark (alternate hap sHemOce1 2021) Hemiscyllium ocellatum GCA_020745765.1_sHemOce1.mat.decon SAMN22550098 PRJNA774309 2021-11-05
26 European common frog Rana temporaria GCF_905171775.1_aRanTem1.1 SAMEA7521635 PRJEB42171 2021-01-28
27 European eel (primary hap 2020) Anguilla anguilla GCF_013347855.1_fAngAng1.pri SAMN12623627 PRJNA561979 2020-06-18
28 fence lizard Sceloporus undulatus GCF_019175285.1_SceUnd_v1.1 SAMN14373011 PRJNA612440 2021-07-08
29 fire-bellied toad (aBomBom1 primary hap 2023) Bombina bombina GCF_027579735.1_aBomBom1.pri SAMN32378350 PRJNA915412 2023-01-09
30 Gaboon caecilian (alternate hap 2019) Geotrypetes seraphini GCA_902459495.1_aGeoSer1.1_alternate_haplotype SAMEA104387963 PRJEB33991 2019-08-18
31 Gaboon caecilian (2019 refseq) Geotrypetes seraphini GCF_902459505.1_aGeoSer1.1 SAMEA104387963 PRJEB33992 2019-08-18
32 gharial Gavialis gangeticus GCF_001723915.1_GavGan_comp1 SAMN03102901 PRJNA172383 2016-09-13
33 Goodes thornscrub tortoise (Sinaloan 2019) Gopherus evgoodei GCF_007399415.2_rGopEvg1_v1.p SAMN03496275 PRJNA489103 2019-07-25
34 Goodes thornscrub tortoise (Sinaloan alternate hap 2019) Gopherus evgoodei GCA_007399395.1_rGopEvg1_v1.alt SAMN03496275 PRJNA489104 2019-07-24
35 gopher snake (HBS135680 alternate hap 2023) Pituophis catenifer annectens GCA_029215685.1_rPitCat1.0.hap2 SAMN33386007 PRJNA937313 2023-03-14
36 gopher snake (HBS135680 primary hap 2023) Pituophis catenifer annectens GCA_029215655.1_rPitCat1.0.hap1 SAMN33386007 PRJNA937314 2023-03-14
37 graceful crag lizard (Gifberg primary hap 2022) Hemicordylus capensis GCF_027244095.1_rHemCap1.1.pri SAMN31669488 PRJNA899811 2022-12-28
38 gray bichir Polypterus senegalus GCF_016835505.1_ASM1683550v1 SAMN13737739 PRJNA599026 2021-02-09
39 great white shark (primary hap 2021) Carcharodon carcharias GCF_017639515.1_sCarCar2.pri SAMN12629504 PRJNA562007 2021-03-30
40 green anole Anolis carolinensis GCF_000090745.1_AnoCar2.0 SAMN02981230 PRJNA18787 2011-01-10
41 green sea turtle (v2 primary hap 2021) Chelonia mydas GCF_015237465.2_rCheMyd1.pri.v2 SAMN12612360 PRJNA561941 2021-07-15
42 High Himalaya frog Nanorana parkeri GCF_000935625.1_ASM93562v1 SAMN02720813 PRJNA243398 2015-03-17
43 Komodo dragon (SLA01 2019) Varanus komodoensis GCF_004798865.1_ASM479886v1 SAMN10967258 PRJNA523222 2019-04-17
44 Lataste's viper (rVipLat1 primary hap 2022) Vipera latastei GCA_024294585.1_rVipLat1.pri SAMN28408464 PRJNA838200 2022-07-20
45 leatherback sea turtle (v4 primary hap 2021 refseq G10K) Dermochelys coriacea GCF_009764565.3_rDerCor1.pri.v4 SAMN12629498 PRJNA561993 2021-08-25
46 leatherback sea turtle (alternate hap 2019) Dermochelys coriacea GCA_009762595.1_rDerCor1.alt SAMN12629498 PRJNA561994 2019-12-18
47 leopard gecko (TG4126 2023) Eublepharis macularius GCF_028583425.1_MPM_Emac_v1.0 SAMN31016422 PRJNA884264 2023-02-10
48 little skate (New England 2023) Leucoraja erinacea GCF_028641065.1_Leri_hhj_1 SAMN23457310 PRJNA783899 2023-02-22
49 loggerhead turtle (SJ_126:Eziel1 2022) Caretta caretta GCF_023653815.1_GSC_CCare_1.0 SAMN27958248 PRJNA826225 2022-06-07
50 mainland tiger snake Notechis scutatus GCF_900518725.1_TS10Xv2-PRI SAMEA4800209 PRJEB27871 2018-09-24
51 marbled whiptail (SIMRID8450 2020) Aspidoscelis marmoratus GCA_014337955.1_AspMar1.0 SAMN06204250 PRJNA360150 2020-08-31
52 meadow viper (primary hap 2022) Vipera ursinii GCA_947247035.1_rVipUrs1.1 SAMEA12832258 PRJEB57183 2022-10-30
53 meadow viper (alternate hap 2022) Vipera ursinii GCA_947247025.1_rVipUrs1.1_alternate_haplotype SAMEA12832258 PRJEB57182 2022-10-30
54 Mexican gopher tortoise (WGS:JAMKFC01 2022) Gopherus flavomarginatus GCF_025201925.1_rGopFla2.mat.asm SAMN24199108 PRJNA794188 2022-09-15
55 Mexican gopher tortoise (WGS:JAMKFD01 2022) Gopherus flavomarginatus GCA_025201965.1_rGopFla2.pat.asm SAMN24199108 PRJNA794189 2022-09-08
56 Mississippi paddlefish Polyodon spathula GCF_017654505.1_ASM1765450v1 SAMN09842169 PRJNA484687 2021-03-31
57 Northern rubber boa (HBS 135849 alternate hap 2022) Charina bottae GCA_023362785.1_rChaBot1.0.a SAMN26367999 PRJNA824888 2022-05-13
58 Northern rubber boa (HBS 135849 primary hap 2022) Charina bottae GCA_023362775.1_rChaBot1.0.p SAMN26367999 PRJNA824889 2022-05-13
59 Northwestern pond turtle (WTP2003 alternate hap 2022) Actinemys marmorata GCA_022086895.1_rActMar1.a SAMN21436765 PRJNA778209 2022-02-08
60 Northwestern pond turtle (WTP2003 primary hap 2022) Actinemys marmorata GCA_022086475.1_rActMar1.p SAMN21436765 PRJNA778210 2022-02-09
61 plains spadefoot toad (aSpeBom1 primary hap 2022) Spea bombifrons GCF_027358695.1_aSpeBom1.2.pri SAMN28408467 PRJNA838345 2022-12-27
62 red-eared slider turtle Trachemys scripta elegans GCF_013100865.1_CAS_Tse_1.0 SAMN12189062 PRJNA552319 2020-05-15
63 Reeves's turtle Mauremys reevesii GCF_016161935.1_ASM1616193v1 SAMN16454374 PRJNA663192 2020-12-22
64 Ringneck snake (HBS135679 primary hap 2022) Diadophis punctatus similis GCA_023053685.1_rDiaPun1.0.p SAMN25872410 PRJNA810488 2022-04-19
65 San Diegan legless lizard (HBS135921 alternate hap 2023) Anniella stebbinsi GCA_029215795.1_rAnnSte1.0.hap2 SAMN33386066 PRJNA938518 2023-03-14
66 San Diegan legless lizard (HBS135921 primary hap 2023) Anniella stebbinsi GCA_029215775.1_rAnnSte1.0.hap1 SAMN33386066 PRJNA938519 2023-03-14
67 San Diegan tiger whiptail (HBS 135688 2022) Aspidoscelis tigris stejnegeri GCA_023333525.1_rAspTig1.0.p SAMN25872408 PRJNA810478 2022-05-11
68 San Diegan tiger whiptail (alternate hap HBS 135688 2022) Aspidoscelis tigris stejnegeri GCA_023333555.1_rAspTig1.0.a SAMN25872408 PRJNA810477 2022-05-11
69 San Diego alligator lizard (HBS135686 alternate hap 2022) Elgaria multicarinata webbii GCA_023053675.1_rElgMul1.0.a SAMN25872353 PRJNA810482 2022-04-19
70 San Diego alligator lizard (HBS135686 primary hap 2022) Elgaria multicarinata webbii GCA_023053635.1_rElgMul1.0.p SAMN25872353 PRJNA810483 2022-04-19
71 San Diego ringneck snake (HBS135679 alternate hap 2022) Diadophis punctatus similis GCA_023053665.1_rDiaPun1.0.a SAMN25872410 PRJNA810487 2022-04-19
72 sand lizard (alternate hap 2019) Lacerta agilis GCA_009819545.1_rLacAgi1.alt SAMN12629509 PRJNA562019 2019-12-23
73 sand lizard (primary hap 2019) Lacerta agilis GCF_009819535.1_rLacAgi1.pri SAMN12629509 PRJNA562018 2019-12-31
74 Schlegel's Japanese gecko Gekko japonicus GCF_001447785.1_Gekko_japonicus_V1.1 SAMN04157958 PRJNA298277 2015-11-25
75 sea lamprey (alternate hap 2020) Petromyzon marinus GCA_010993595.1_kPetMar1.alt SAMN12629506 PRJNA562012 2020-02-24
76 sea lamprey (primary hap 2020) Petromyzon marinus GCF_010993605.1_kPetMar1.pri SAMN12629506 PRJNA562011 2020-02-24
77 smaller spotted catshark Scyliorhinus canicula GCF_902713615.1_sScyCan1.1 SAMEA994730 PRJEB35945 2020-12-17
78 smalltooth sawfish (primary hap 2019 refseq) Pristis pectinata GCF_009764475.1_sPriPec2.1.pri SAMN12629505 PRJNA562009 2019-12-19
79 smalltooth sawfish (alternate hap 2019) Pristis pectinata GCA_009764485.1_sPriPec2.alt SAMN12629505 PRJNA562010 2019-12-18
80 Southern Pacific rattlesnake (HBS135844 alternate hap 2022) Crotalus oreganus helleri GCA_024509165.1_rCroOre1.a SAMN25872349 PRJNA807341 2022-08-03
81 Southern Pacific rattlesnake (HBS135844 primary hap 2022) Crotalus oreganus helleri GCA_024509115.1_rCroOre1.0.p SAMN25872349 PRJNA807342 2022-08-04
82 Southwestern pond turtle (HBS135687 alternate hap 2022) Actinemys pallida GCA_023634275.1_rActPal1.0.a SAMN25872472 PRJNA810503 2022-06-01
83 Southwestern pond turtle (HBS135687 primary hap 2022) Actinemys pallida GCA_023634205.1_rActPal1.0.p SAMN25872472 PRJNA810504 2022-06-01
84 spotted gar Lepisosteus oculatus GCF_000242695.1_LepOcu1 SAMN00706774 PRJNA68247 2012-01-13
85 sterlet (fAciRut3.2 2022) Acipenser ruthenus GCA_902713435.2_fAciRut3.2_paternal_haplotype SAMEA5572864 PRJEB35913 2022-02-01
86 sterlet (v2 Gen_M01 2020) Acipenser ruthenus GCF_010645085.2_ASM1064508v2 SAMN12612932 PRJNA561280 2020-02-19
87 thorny skate (primary hap CabotCenter1 v1.1 2020) Amblyraja radiata GCF_010909765.2_sAmbRad1.1.pri SAMN09948523 PRJNA591369 2020-02-21
88 thorny skate (alternate hap CabotCenter1 2020) Amblyraja radiata GCA_010909745.1_sAmbRad1.alt SAMN09948523 PRJNA591368 2020-02-14
89 three-toed box turtle Terrapene carolina triunguis GCF_002925995.2_T_m_triunguis-2.0 SAMN08285364 PRJNA415469 2018-09-21
90 tiger rattlesnake Crotalus tigris GCF_016545835.1_ASM1654583v1 SAMN12497667 PRJNA558767 2021-01-06
91 tiny Cayenne caecilian Microcaecilia unicolor GCF_901765095.1_aMicUni1.1 SAMEA104387962 PRJEB32737 2019-06-22
92 tiny Cayenne caecilian (alternate hap 2019) Microcaecilia unicolor GCA_901765105.1_aMicUni1.1_alternate_haplotype SAMEA104387962 PRJEB32738 2019-07-08
93 Townsend's dwarf sphaero (gecko TG3544 2022) Sphaerodactylus townsendi GCF_021028975.2_MPM_Stown_v2.3 SAMN20179316 PRJNA746057 2022-04-08
94 tropical clawed frog Xenopus tropicalis GCF_000004195.4_UCB_Xtro_10.0 SAMN13041969 PRJNA577946 2019-11-14
95 two-lined caecilian (2019) Rhinatrema bivittatum GCF_901001135.1_aRhiBiv1.1 SAMEA104387956 PRJEB32111 2019-06-02
96 two-lined caecilian (alternate hap 2019) Rhinatrema bivittatum GCA_901001175.1_aRhiBiv1.1_alternate_haplotype SAMEA104387956 PRJEB32112 2019-06-02
97 valley gartersnake (HBS 135685 alternate hap 2023) Thamnophis sirtalis fitchi GCA_029207655.1_rThaSir1.0.hap2 SAMN26367981 PRJNA913137 2023-03-14
98 valley gartersnake (HBS 135685 primary hap 2023) Thamnophis sirtalis fitchi GCA_029207665.1_rThaSir1.0.hap1 SAMN26367981 PRJNA913138 2023-03-14
99 viviparous/common lizard Zootoca vivipara GCF_011800845.1_UG_Zviv_1 SAMN14329711 PRJNA610958 2020-04-01
100 West African lungfish Protopterus annectens GCF_019279795.1_PAN1.0 SAMN17890435 PRJNA701604 2021-07-20
101 western fence lizard (IW3139 2022) Sceloporus occidentalis GCA_023333635.1_rSceOcc1.0.a SAMN27480378 PRJNA824882 2022-05-11
102 western fence lizard (IW3139 primary hap 2022) Sceloporus occidentalis GCA_023333645.1_rSceOcc1.0.p SAMN27480378 PRJNA824883 2022-05-11
103 western painted turtle (v5 RCT428 2020) Chrysemys picta bellii GCF_000241765.5_Chrysemys_picta_BioNano-3.0.4 SAMN02713681 PRJNA78657 2020-08-21
104 western red-tailed skink (HBS 135693 alternate hap 2022) Plestiodon gilberti rubricaudatus GCA_026170595.1_rPleGil1.0.hap2 SAMN30523592 PRJNA874060 2022-11-14
105 western red-tailed skink (HBS 135693 primary hap 2022) Plestiodon gilberti rubricaudatus GCA_026170395.1_rPleGil1.0.hap1 SAMN30523592 PRJNA874061 2022-11-14
106 western spadefoot toad (HBS 135690 2023) Spea hammondii GCA_029215705.1_aSpeHam1.0.hap1 SAMN33386125 PRJNA938521 2023-03-15
107 western spadefoot toad (HBS 135690 2023) Spea hammondii GCA_029215755.1_aSpeHam1.0.hap2 SAMN33386125 PRJNA938520 2023-03-14
108 western terrestrial garter snake (alternate hap 2019) Thamnophis elegans GCA_009769695.1_rThaEle1.alt SAMN12629499 PRJNA561997 2019-12-19
109 western terrestrial garter snake (primary hap 2019) Thamnophis elegans GCF_009769535.1_rThaEle1.pri SAMN12629499 PRJNA561996 2019-12-23
110 whale shark (Ralph 2017 Emory U) Rhincodon typus GCF_001642345.1_ASM164234v2 SAMN04562461 PRJNA255419 2017-03-03
111 whale shark (14 2022 Squalomix) Rhincodon typus GCF_021869965.1_sRhiTyp1.1 SAMN19519256 PRJNA703743 2022-02-03
112 whitespotted bambooshark Chiloscyllium plagiosum GCF_004010195.1_ASM401019v2 SAMN09508879 PRJNA478295 2019-01-10
113 yellowpond turtle (Southern MM-2020 2021) Mauremys mutica GCF_020497125.1_ASM2049712v1 SAMN19136605 PRJNA729638 2021-10-14
114 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 159 assemblies assembly stats track stats
Mammals 407 assemblies assembly stats track stats
Birds 270 assemblies assembly stats track stats
Fishes 270 assemblies assembly stats track stats
other vertebrates 114 assemblies assembly stats track stats
Invertebrates 583 assemblies assembly stats track stats
Plants 230 assemblies assembly stats track stats
Fungi 544 assemblies assembly stats track stats
Viruses 259 assemblies assembly stats track stats
Bacteria 64 assemblies assembly stats track stats
legacy/superseded 336 assemblies assembly stats track stats
collections below are subsets of the assemblies above
VGP - Vertebrate Genome Project 445 assemblies assembly stats track stats
CCGP - The California Conservation Genomics Project 126 assemblies assembly stats track stats
HPRC - Human Pangenome Reference Consortium 96 assemblies assembly stats track stats