VGP - Vertebrate Genomes Project assembly hub

VGP logo

This assembly hub contains assemblies released by the Vertebrate Genomes Project. (set of legacy/superseded assemblies)

How to view the assembly of interest

The links to the genome browser in the table below will attach that one specific assembly to the genome browser. Use the links in the column labeled common name and view in browser to view that assembly in the genome browser.

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


Cite reference: To reference these resources in publications, please credit:

Clawson, H., Lee, B.T., Raney, B.J. et al. "GenArk: towards a million UCSC genome browsers.
Genome Biol 24, 217 (2023). https://doi.org/10.1186/s13059-023-03057-x

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 class VGP link provides access to the VGP GenomeArk page for that genome.
The other links provide access to NCBI resources for these assemblies.
count common name and
view in UCSC browser
[IGV browser]
scientific name
and data download
NCBI assembly BioSample BioProject assembly date,
source link
class
VGP link
1 African grass rat (paternal X 2020)[IGV] Arvicanthis niloticus GCA_011762505.1_mArvNil1.pat.X SAMN12611849 PRJNA608735 2020-03-27 mammals
2 Atlantic halibut (genbank)[IGV] Hippoglossus hippoglossus GCA_009819705.1_fHipHip1.pri SAMN12629501 PRJNA562001 2019-12-31 fish
3 Anna's hummingbird[IGV] Calypte anna GCF_003957555.1_bCalAnn1_v1.p SAMN02265252 PRJNA489139 2019-05-16 birds
4 barn swallow (bHirRus1 v2 primary hap 2021 refseq)[IGV] Hirundo rustica GCF_015227805.1_bHirRus1.pri.v2 SAMN14675488 PRJNA636192 2021-03-02 birds
5 black rhinoceros (mBicDic1 primary hap 2021 genbank)[IGV] Diceros bicornis minor GCA_020826845.1_mDicBic1.mat.cur SAMN22047685 PRJNA773944 2021-11-10 mammals
6 black-legged kittiwake (bRisTri1.patW 2023 genbank)[IGV] Rissa tridactyla GCA_028500815.1_bRisTri1.patW.cur.20221130 SAMN32104255 PRJNA909853 2023-02-09 birds
7 blue whale (JJ_BM4_2016_0621 v2 2020)[IGV] Balaenoptera musculus GCA_009873245.2_mBalMus1.v2 SAMN12287136 PRJNA554522 2020-02-03 mammals
8 blue whale (alternate hap JJ_BM4_2016_0621 2019)[IGV] Balaenoptera musculus GCA_008658375.1_mBalMus1_alternate SAMN12287136 PRJNA554523 2019-09-23 mammals
9 blunt-snouted clingfish (v1 2019 genbank)[IGV] Gouania willdenowi GCA_900634775.1_fGouWil2.1 SAMEA104026382 PRJEB30359 2019-02-06 fish
10 blunt-snouted clingfish (v1 2019 refseq)[IGV] Gouania willdenowi GCF_900634775.1_fGouWil2.1 SAMEA104026382 PRJEB30359 2019-02-06 fish
11 Bornean orangutan (v1 AG05252 alternate hap 2023 genbank)[IGV] Pongo pygmaeus GCA_028885525.1_NHGRI_mPonPyg2-v1.1-hic.freeze_alt SAMN10521809 PRJNA916740 2023-02-28 primates
12 Bornean orangutan (v1 AG05252 primary hap 2023 refseq)[IGV] Pongo pygmaeus GCF_028885625.1_NHGRI_mPonPyg2-v1.1-hic.freeze_pri SAMN10521809 PRJNA916742 2023-02-28 primates
13 budgerigar[IGV] Melopsittacus undulatus GCA_012275295.1_bMelUnd1.mat.Z SAMN12623090 PRJNA612327 2020-04-13 birds
14 California sea lion (v1 2019)[IGV] Zalophus californianus GCA_009762305.1_mZalCal1.pri SAMN12368149 PRJNA559673 2019-12-18 mammals
15 California sea lion (alternate hap 2019)[IGV] Zalophus californianus GCA_009762295.1_mZalCal1.alt SAMN12368149 PRJNA559674 2019-12-17 mammals
16 Canada lynx (LIC74 v1 2019)[IGV] Lynx canadensis GCF_007474595.1_mLynCan4_v1.p SAMN09948483 PRJNA489107 2019-07-26 mammals
17 Canada lynx (alternate hap LIC74 2019)[IGV] Lynx canadensis GCA_007474575.1_mLynCan4_v1.alt SAMN09948483 PRJNA489108 2019-07-25 mammals
18 channel bull blenny[IGV] Cottoperca gobio GCA_900634415.1_fCotGob3.1 SAMEA104242975 PRJEB30248 2019-02-06 fish
19 chimpanzee (v1 AG18354 alternate hap 2023 genbank)[IGV] Pan troglodytes GCA_028858805.1_NHGRI_mPanTro3-v1.1-hic.freeze_alt SAMN30216104 PRJNA916737 2023-02-27 primates
20 chimpanzee (v1 AG18354 primary hap 2023 refseq)[IGV] Pan troglodytes GCF_028858775.1_NHGRI_mPanTro3-v1.1-hic.freeze_pri SAMN30216104 PRJNA916736 2023-02-27 primates
21 climbing perch (v1.2 2018 genbank)[IGV] Anabas testudineus GCA_900324465.2_fAnaTes1.2 SAMEA104026376 PRJEB25768 2018-12-19 fish
22 climbing perch (v1.2 2018 refseq)[IGV] Anabas testudineus GCF_900324465.2_fAnaTes1.2 SAMEA104026376 PRJEB25768 2018-12-19 fish
23 common brushtail (genbank 2020)[IGV] Trichosurus vulpecula GCA_011100635.1_mTriVul1.pri SAMN12629507 PRJNA562014 2020-03-10 mammals
24 common bottlenose dolphin (maternal Y genbank 2020)[IGV] Tursiops truncatus GCA_011762595.1_mTurTru1.mat.Y SAMN12326775 PRJNA608726 2020-03-27 mammals
25 common cuckoo (bCucCan1 primary hap 2021 genbank)[IGV] Cuculus canorus GCA_017976375.1_bCucCan1.pri SAMN12629508 PRJNA562015 2021-04-15 birds
26 common swift (bApuApu2 2021 genbank)[IGV] Apus apus GCA_020740795.1_bApuApu2.pri.cur SAMN22785356 PRJNA776336 2021-11-04 birds
27 denticle herring (v1 2019)[IGV] Denticeps clupeoides GCF_900700375.1_fDenClu1.1 SAMEA104129917 PRJEB31545 2019-03-16 fish
28 downy woodpecker (bDryPub1 primary hap 2020)[IGV] Dryobates pubescens GCA_014839835.1_bDryPub1.pri SAMN12629497 PRJNA561991 2020-10-02 birds
29 eastern happy (v2 2018)[IGV] Astatotilapia calliptera GCF_900246225.1_fAstCal1.2 SAMEA104026430 PRJEB24325 2018-05-30 fish
30 emu (v1 ZJU1.0 2020)[IGV] Dromaius novaehollandiae GCA_016128335.1_ZJU1.0 SAMN15183959 PRJNA638233 2020-12-20 birds
31 epaulette shark (sHemOce1 2021 genbank)[IGV] Hemiscyllium ocellatum GCA_020745735.1_sHemOce1.pat.X.cur. SAMN22550098 PRJNA774310 2021-11-05 sharks
32 Eurasian red squirrel (v1.1 2019)[IGV] Sciurus vulgaris GCA_902686455.1_mSciVul1.1 SAMEA994733 PRJEB35380 2019-11-26 mammals
33 Eurasian water vole (v1 2020)[IGV] Arvicola amphibius GCF_903992535.1_mArvAmp1.1 SAMEA994740 PRJEB39550 2020-08-06 mammals
34 European turtle dove (v1.1 primary hap 2019)[IGV] Streptopelia turtur GCA_901699155.1_bStrTur1.1 SAMEA994735 PRJEB32724 2019-06-05 birds
35 European turtle dove[IGV] Streptopelia turtur GCA_901699165.1_bStrTur1.1_alternate_haplotype SAMEA994735 PRJEB32725 2019-06-02 birds
36 European woodmouse (2022 genbank)[IGV] Apodemus sylvaticus GCA_947179515.1_mApoSyl1.1 SAMEA7702024 PRJEB56948 2022-10-28 mammals
37 flier cichlid[IGV] Archocentrus centrarchus GCA_007364275.2_fArcCen1 SAMN09948522 PRJNA489129 2019-08-01 fish
38 Gabon caecilian[IGV] Geotrypetes seraphini GCA_902459505.1_aGeoSer1.1 SAMEA104387963 PRJEB33992 2019-08-18 amphibians
39 gilthead seabream (v1 2019)[IGV] Sparus aurata GCF_900880675.1_fSpaAur1.1 SAMEA104384835 PRJEB31901 2019-07-30 fish
40 golden eagle (2019)[IGV] Aquila chrysaetos chrysaetos GCF_900496995.1_bAquChr1.2 SAMEA994725 PRJEB27699 2019-07-08 birds
41 golden eagle (v1.2 alternate hap 2019)[IGV] Aquila chrysaetos chrysaetos GCA_902153765.1_bAquChr1.2_alternate_haplotype SAMEA994725 PRJEB33298 2019-07-08 birds
42 greater horseshoe bat (v1 MPI-CBG 2019 genbank)[IGV] Rhinolophus ferrumequinum GCA_004115265.2_mRhiFer1_v1.p SAMN09948510 PRJNA489106 2019-05-16 mammals
43 greater horseshoe bat (v1 MPI-CBG 2019 refseq)[IGV] Rhinolophus ferrumequinum GCF_004115265.1_mRhiFer1_v1.p SAMN09948510 PRJNA489106 2019-05-16 mammals
44 greater pipefish[IGV] Syngnathus acus GCA_901709675.1_fSynAcu1.1 SAMEA104381750 PRJEB32741 2019-05-29 fish
45 green sea turtle (v1 2020)[IGV] Chelonia mydas GCF_015237465.1_rCheMyd1.pri SAMN12612360 PRJNA561941 2020-11-05 reptiles
46 Indian glassy fish (v1 2019)[IGV] Parambassis ranga GCF_900634625.1_fParRan2.1 SAMEA4675621 PRJEB30257 2019-02-06 fish
47 kakapo[IGV] Strigops habroptila GCA_004027225.2_bStrHab1.2.pri SAMN09948751 PRJNA489135 2020-03-04 birds
48 Korean giant-fin mudskipper (v1 primary hap 2020 genbank)[IGV] Periophthalmus magnuspinnatus GCA_009829125.1_fPerMag1.pri SAMN12629500 PRJNA561998 2020-01-03 fish
49 Korean giant-fin mudskipper (v1 primary hap 2020 refseq)[IGV] Periophthalmus magnuspinnatus GCF_009829125.1_fPerMag1.pri SAMN12629500 PRJNA561998 2020-01-03 fish
50 lanner falcon (bFalBia1 primary hap 2022 genbank)[IGV] Falco biarmicus GCA_023638135.1_bFalBia1.pri SAMN28688289 PRJNA842826 2022-06-02 birds
51 leatherback sea turtle (v1 2019 genbank G10K)[IGV] Dermochelys coriacea GCA_009764565.1_rDerCor1.pri SAMN12629498 PRJNA561993 2019-12-19 reptiles
52 leatherback sea turtle (v3 2020 refseq G10K)[IGV] Dermochelys coriacea GCF_009764565.2_rDerCor1.pri.v3 SAMN12629498 PRJNA561993 2020-12-09 reptiles
53 leatherback sea turtle (v1 alternate hap 2020)[IGV] Dermochelys coriacea GCA_009762595.1_rDerCor1.alt SAMN12629498 PRJNA561994 2019-12-18 reptiles
54 lesser kestrel (v1 2021)[IGV] Falco naumanni GCF_017639655.1_bFalNau1.pat SAMN16870685 PRJNA702666 2021-03-30 birds
55 lesser rhea (bPtePen1 primary hap 2023 genbank)[IGV] Rhea pennata GCA_028389875.1_bPtePen1.pri SAMN32606345 PRJNA918801 2023-02-06 birds
56 live sharksucker (v1 2019)[IGV] Echeneis naucrates GCF_900963305.1_fEcheNa1.1 SAMEA4966390 PRJEB31992 2019-04-11 fish
57 lumpfish (genbank)[IGV] Cyclopterus lumpus GCA_009769545.1_fCycLum1.pri SAMN12629502 PRJNA562003 2019-12-23 fish
58 mute swan (2019)[IGV] Cygnus olor GCA_009769625.1_bCygOlo1.pri SAMN12621369 PRJNA561960 2019-12-23 birds
59 mute swan (bCygOlo1 v1 alternate hap 2019)[IGV] Cygnus olor GCA_009769485.1_bCygOlo1.alt SAMN12621369 PRJNA561961 2019-12-19 birds
60 Nelson's sparrow (bAmmNel1 primary hap 2023 genbank)[IGV] Ammospiza nelsoni GCA_027579445.1_bAmmNel1.pri SAMN28421656 PRJNA839456 2023-01-09 birds
61 New Zealand spotty (genbank)[IGV] Notolabrus celidotus GCA_009762535.1_fNotCel1.pri SAMN12623201 PRJNA561956 2019-12-18 fish
62 North Atlantic right whale (hap2 2023 genbank)[IGV] Eubalaena glacialis GCA_028564815.1_mEubGla1.hap2 SAMN32746534 PRJNA924128 2023-02-09 mammals
63 northern pike[IGV] Esox lucius GCA_011004845.1_fEsoLuc1.pri SAMN12623624 PRJNA561977 2020-03-05 fish
64 pale spear-nosed bat (MPI-MPIP v1 2019)[IGV] Phyllostomus discolor GCF_004126475.1_mPhyDis1_v1.p SAMN09948786 PRJNA489141 2019-02-07 mammals
65 pale spear-nosed bat (alternate hap MPI-MPIP 2019)[IGV] Phyllostomus discolor GCA_004115245.1_mPhyDis1_v1.h SAMN09948786 PRJNA489142 2019-01-28 mammals
66 peregrine falcon (bFalPer1 primary hap 2022 genbank)[IGV] Falco peregrinus GCA_023634155.1_bFalPer1.pri SAMN28688290 PRJNA842834 2022-06-02 birds
67 platypus (Pmale09 v3 2020)[IGV] Ornithorhynchus anatinus GCA_004115215.3_mOrnAna1.pri.v3 SAMN08537700 PRJNA489114 2020-04-13 mammals
68 prehistoric monster fish[IGV] Thalassophryne amazonica GCA_902500255.1_fThaAma1.1 SAMEA104129913 PRJEB34606 2019-09-30 fish
69 pygmy chimpanzee (v1 primary hap 2023)[IGV] Pan paniscus GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri SAMN13935689 PRJNA942951 2023-03-20 primates
70 pygmy sperm whale (mKogBre1 haplotype 1 2022 genbank)[IGV] Kogia breviceps GCA_026419965.1_mKogBre1_haplotype_1 SAMN31719513 PRJNA901930 2022-11-27 mammals
71 reedfish (v1 alternate hap 2019)[IGV] Erpetoichthys calabaricus GCA_900700845.2_fErpCal1.1_alternate_haplotype SAMEA104026374 PRJEB31582 2019-03-27 fish
72 reedfish (2019)[IGV] Erpetoichthys calabaricus GCF_900747795.1_fErpCal1.1 SAMEA104026374 PRJEB31579 2019-03-26 fish
73 river trout (v1 2019)[IGV] Salmo trutta GCF_901001165.1_fSalTru1.1 SAMEA994732 PRJEB32115 2019-06-02 fish
74 rock pigeon (v1 racing homer 2024)[IGV] Columba livia GCA_036013475.1_bColLiv1.pat.W SAMN38891892 PRJNA1054131 2024-01-31 birds
75 Saker falcon (bFalChe1 primary hap 2022 genbank)[IGV] Falco cherrug GCA_023634085.1_bFalChe1.pri SAMN28688204 PRJNA842831 2022-06-02 birds
76 saltmarsh sparrow (bAmmCau1 primary hap 2023 genbank)[IGV] Ammospiza caudacuta GCA_027887145.1_bAmmCau1.pri SAMN28421630 PRJNA839452 2023-01-18 birds
77 San Diego alligator lizard (v1.0 HBS135686 primary hap 2022)[IGV] Elgaria multicarinata webbii GCA_023053635.1_rElgMul1.0.p SAMN25872353 PRJNA810483 2022-04-19 reptiles
78 San Diego alligator lizard (v1.1 HBS135686 primary hap 2024 genbank)[IGV] Elgaria multicarinata webbii GCA_023053635.2_rElgMul1.1.pri SAMN25872353 PRJNA810483 2024-01-04 reptiles
79 siamang (v1 Jambi primary hap 2023)[IGV] Symphalangus syndactylus GCF_028878055.1_NHGRI_mSymSyn1-v1.1-hic.freeze_pri SAMN30216103 PRJNA916729 2023-02-28 primates
80 Siamese fighting fish (v1 alternate hap 2019)[IGV] Betta splendens GCA_900651605.1_fBetSpl5.1_alternate_haplotype SAMEA104381735 PRJEB30366 2019-02-07 fish
81 Siamese fighting fish (v2 primary hap 2019)[IGV] Betta splendens GCF_900634795.2_fBetSpl5.2 SAMEA104381735 PRJEB30365 2019-03-20 fish
82 Siamese fighting fish (v3 primary hap 2020)[IGV] Betta splendens GCF_900634795.3_fBetSpl5.3 SAMEA104381735 PRJEB30365 2020-08-25 fish
83 smalltooth sawfish (v2 2019 genbank)[IGV] Pristis pectinata GCA_009764475.1_sPriPec2.pri SAMN12629505 PRJNA562009 2019-12-19 sharks
84 sterlet (paternal 2020)[IGV] Acipenser ruthenus GCA_902713435.1_fAciRut3.1_paternal_haplotype SAMEA5572864 PRJEB35913 2020-01-08 fish
85 Sumatran orangutan (v1 AG06213 primary hap 2023)[IGV] Pongo abelii GCF_028885655.1_NHGRI_mPonAbe1-v1.1-hic.freeze_pri SAMN10521808 PRJNA916743 2023-02-28 primates
86 Swainson's thrush (v1 2019)[IGV] Catharus ustulatus GCF_009819885.1_bCatUst1.pri SAMN12618602 PRJNA561933 2019-12-31 birds
87 Swainson's thrush (bCatUst1 v1 alternate hap 2019)[IGV] Catharus ustulatus GCA_009819505.1_bCatUst1.alt SAMN12618602 PRJNA561934 2019-12-23 birds
88 swamp sparrow (bMelGeo1 primary hap 2023 genbank)[IGV] Melospiza georgiana GCA_028018845.1_bMelGeo1.pri SAMN22787412 PRJNA915609 2023-01-31 birds
89 thorny skate (genbank 2020)[IGV] Amblyraja radiata GCA_010909765.1_sAmbRad1.pri SAMN09948523 PRJNA591369 2020-02-21 sharks
90 thorny skate (v1 2020)[IGV] Amblyraja radiata GCF_010909765.1_sAmbRad1.pri SAMN09948523 PRJNA591369 2020-02-21 sharks
91 torafugu (fTakRub1.2 2019 refseq)[IGV] Takifugu rubripes GCF_901000725.2_fTakRub1.2 SAMEA104384834 PRJEB31988 2019-06-05 fish
92 village indigobird (merged hap OUT-0048 2022 genbank)[IGV] Vidua chalybeata GCA_026979565.1_bVidCha1_merged_haplotype SAMN12254000 PRJNA889055 2022-12-21 birds
93 western lowland gorilla (v1 KB3781 2023)[IGV] Gorilla gorilla gorilla GCF_029281585.1_NHGRI_mGorGor1-v1.1-0.2.freeze_pri SAMN04003007 PRJNA942267 2023-03-20 primates
94 white leghorn X broiler chicken (v1 leghorn haplotype v1 2021)[IGV] Gallus gallus GCF_016700215.1_bGalGal1.pat.whiteleghornlayer.GRCg7w SAMN15960293 PRJNA660758 2021-01-19 birds
95 white-tufted-ear marmoset (v1 paternal 2020)[IGV] Callithrix jacchus GCA_011100535.1_mCalJac1.pat SAMN12368443 PRJNA558087 2020-03-10 primates
96 zebra finch (genbank 2020 Blue55 female)[IGV] Taeniopygia guttata GCA_009859065.2_bTaeGut2.pri.v2 SAMN09946140 PRJNA489186 2020-04-01 birds
97 zebra finch (refseq 2019 Black17 male)[IGV] Taeniopygia guttata GCF_003957565.1_bTaeGut1_v1.p SAMN02981239 PRJNA489098 2019-05-16 birds
98 zebra finch (genbank 2019 Black17 male)[IGV] Taeniopygia guttata GCA_003957565.2_bTaeGut1_v1.p SAMN02981239 PRJNA489098 2019-05-16 birds
99 zebra finch (alternate hap Black17 2018)[IGV] Taeniopygia guttata GCA_003957525.1_bTaeGut1_v1.h SAMN02981239 PRJNA489099 2018-12-20 birds
100 zig-zag eel (v1.2 2019 refseq)[IGV] Mastacembelus armatus GCF_900324485.2_fMasArm1.2 SAMEA104026378 PRJEB25769 2019-03-16 fish

Alternate sets of VGP assembliesNCBI Refseq
Index pages:  primary assembly alternate/haplotype trio mat/pat legacy/superseded other NCBI Refseq assemblies
Assembly statistics:  primary assembly alternate/haplotype trio mat/pat legacy/superseded other NCBI Refseq assemblies
Track statistics:  primary assembly alternate/haplotype trio mat/pat legacy/superseded other NCBI Refseq assemblies