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 (set of legacy/superseded assemblies)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 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/VGP/legacyHub.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 VGP 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.


Listings:

  (from RepeatModeler masking)

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 browser
scientific name
and data download
NCBI assembly BioSample BioProject assembly date,
source link
class
VGP link
1 African grass rat (paternal X 2020) Arvicanthis niloticus GCA_011762505.1_mArvNil1.pat.X SAMN12611849 PRJNA608735 2020-03-27 mammals
2 Atlantic halibut (genbank) Hippoglossus hippoglossus GCA_009819705.1_fHipHip1.pri SAMN12629501 PRJNA562001 2019-12-31 fish
3 Anna's hummingbird Calypte anna GCF_003957555.1_bCalAnn1_v1.p SAMN02265252 PRJNA489139 2019-05-16 birds
4 barn swallow (bHirRus1 v2 primary hap 2021 refseq) Hirundo rustica GCF_015227805.1_bHirRus1.pri.v2 SAMN14675488 PRJNA636192 2021-03-02 birds
5 black-legged kittiwake (bRisTri1.patW 2023 genbank) Rissa tridactyla GCA_028500815.1_bRisTri1.patW.cur.20221130 SAMN32104255 PRJNA909853 2023-02-09 birds
6 blue whale (JJ_BM4_2016_0621 v2 2020) Balaenoptera musculus GCA_009873245.2_mBalMus1.v2 SAMN12287136 PRJNA554522 2020-02-03 mammals
7 blue whale (alternate hap JJ_BM4_2016_0621 2019) Balaenoptera musculus GCA_008658375.1_mBalMus1_alternate SAMN12287136 PRJNA554523 2019-09-23 mammals
8 blunt-snouted clingfish (v1 2019 genbank) Gouania willdenowi GCA_900634775.1_fGouWil2.1 SAMEA104026382 PRJEB30359 2019-02-06 fish
9 blunt-snouted clingfish (v1 2019 refseq) Gouania willdenowi GCF_900634775.1_fGouWil2.1 SAMEA104026382 PRJEB30359 2019-02-06 fish
10 budgerigar Melopsittacus undulatus GCA_012275295.1_bMelUnd1.mat.Z SAMN12623090 PRJNA612327 2020-04-13 birds
11 California sea lion (v1 2019) Zalophus californianus GCA_009762305.1_mZalCal1.pri SAMN12368149 PRJNA559673 2019-12-18 mammals
12 California sea lion (alternate hap 2019) Zalophus californianus GCA_009762295.1_mZalCal1.alt SAMN12368149 PRJNA559674 2019-12-17 mammals
13 Canada lynx (LIC74 v1 2019) Lynx canadensis GCF_007474595.1_mLynCan4_v1.p SAMN09948483 PRJNA489107 2019-07-26 mammals
14 Canada lynx (alternate hap LIC74 2019) Lynx canadensis GCA_007474575.1_mLynCan4_v1.alt SAMN09948483 PRJNA489108 2019-07-25 mammals
15 channel bull blenny Cottoperca gobio GCA_900634415.1_fCotGob3.1 SAMEA104242975 PRJEB30248 2019-02-06 fish
16 climbing perch (v1.2 2018 genbank) Anabas testudineus GCA_900324465.2_fAnaTes1.2 SAMEA104026376 PRJEB25768 2018-12-19 fish
17 climbing perch (v1.2 2018 refseq) Anabas testudineus GCF_900324465.2_fAnaTes1.2 SAMEA104026376 PRJEB25768 2018-12-19 fish
18 common brushtail (genbank 2020) Trichosurus vulpecula GCA_011100635.1_mTriVul1.pri SAMN12629507 PRJNA562014 2020-03-10 mammals
19 common bottlenose dolphin (maternal Y genbank 2020) Tursiops truncatus GCA_011762595.1_mTurTru1.mat.Y SAMN12326775 PRJNA608726 2020-03-27 mammals
20 common cuckoo (bCucCan1 primary hap 2021 genbank) Cuculus canorus GCA_017976375.1_bCucCan1.pri SAMN12629508 PRJNA562015 2021-04-15 birds
21 common swift (bApuApu2 2021 genbank) Apus apus GCA_020740795.1_bApuApu2.pri.cur SAMN22785356 PRJNA776336 2021-11-04 birds
22 denticle herring (v1 2019) Denticeps clupeoides GCF_900700375.1_fDenClu1.1 SAMEA104129917 PRJEB31545 2019-03-16 fish
23 downy woodpecker (bDryPub1 primary hap 2020) Dryobates pubescens GCA_014839835.1_bDryPub1.pri SAMN12629497 PRJNA561991 2020-10-02 birds
24 eastern happy (v2 2018) Astatotilapia calliptera GCF_900246225.1_fAstCal1.2 SAMEA104026430 PRJEB24325 2018-05-30 fish
25 emu (v1 ZJU1.0 2020) Dromaius novaehollandiae GCA_016128335.1_ZJU1.0 SAMN15183959 PRJNA638233 2020-12-20 birds
26 Eurasian water vole (v1 2020) Arvicola amphibius GCF_903992535.1_mArvAmp1.1 SAMEA994740 PRJEB39550 2020-08-06 mammals
27 Eurasian water vole (v2 2021) Arvicola amphibius GCF_903992535.2_mArvAmp1.2 SAMEA994740 PRJEB39550 2021-05-15 mammals
28 European turtle dove (v1.1 primary hap 2019) Streptopelia turtur GCA_901699155.1_bStrTur1.1 SAMEA994735 PRJEB32724 2019-06-05 birds
29 European turtle dove Streptopelia turtur GCA_901699165.1_bStrTur1.1_alternate_haplotype SAMEA994735 PRJEB32725 2019-06-02 birds
30 European woodmouse (2022 genbank) Apodemus sylvaticus GCA_947179515.1_mApoSyl1.1 SAMEA7702024 PRJEB56948 2022-10-28 mammals
31 flier cichlid Archocentrus centrarchus GCA_007364275.2_fArcCen1 SAMN09948522 PRJNA489129 2019-08-01 fish
32 Gabon caecilian Geotrypetes seraphini GCA_902459505.1_aGeoSer1.1 SAMEA104387963 PRJEB33992 2019-08-18 amphibians
33 gilthead seabream (v1 2019) Sparus aurata GCF_900880675.1_fSpaAur1.1 SAMEA104384835 PRJEB31901 2019-07-30 fish
34 golden eagle (2019) Aquila chrysaetos chrysaetos GCF_900496995.1_bAquChr1.2 SAMEA994725 PRJEB27699 2019-07-08 birds
35 golden eagle (v1.2 alternate hap 2019) Aquila chrysaetos chrysaetos GCA_902153765.1_bAquChr1.2_alternate_haplotype SAMEA994725 PRJEB33298 2019-07-08 birds
36 greater horseshoe bat (v1 MPI-CBG 2019 genbank) Rhinolophus ferrumequinum GCA_004115265.2_mRhiFer1_v1.p SAMN09948510 PRJNA489106 2019-05-16 mammals
37 greater horseshoe bat (v1 MPI-CBG 2019 refseq) Rhinolophus ferrumequinum GCF_004115265.1_mRhiFer1_v1.p SAMN09948510 PRJNA489106 2019-05-16 mammals
38 greater pipefish Syngnathus acus GCA_901709675.1_fSynAcu1.1 SAMEA104381750 PRJEB32741 2019-05-29 fish
39 green sea turtle (v1 2020) Chelonia mydas GCF_015237465.1_rCheMyd1.pri SAMN12612360 PRJNA561941 2020-11-05 reptiles
40 Indian glassy fish (v1 2019) Parambassis ranga GCF_900634625.1_fParRan2.1 SAMEA4675621 PRJEB30257 2019-02-06 fish
41 kakapo Strigops habroptila GCA_004027225.2_bStrHab1.2.pri SAMN09948751 PRJNA489135 2020-03-04 birds
42 Korean giant-fin mudskipper (v1 primary hap 2020 genbank) Periophthalmus magnuspinnatus GCA_009829125.1_fPerMag1.pri SAMN12629500 PRJNA561998 2020-01-03 fish
43 Korean giant-fin mudskipper (v1 primary hap 2020 refseq) Periophthalmus magnuspinnatus GCF_009829125.1_fPerMag1.pri SAMN12629500 PRJNA561998 2020-01-03 fish
44 leatherback sea turtle (v1 2019 genbank G10K) Dermochelys coriacea GCA_009764565.1_rDerCor1.pri SAMN12629498 PRJNA561993 2019-12-19 reptiles
45 leatherback sea turtle (v3 2020 refseq G10K) Dermochelys coriacea GCF_009764565.2_rDerCor1.pri.v3 SAMN12629498 PRJNA561993 2020-12-09 reptiles
46 lesser kestrel (v1 2021) Falco naumanni GCF_017639655.1_bFalNau1.pat SAMN16870685 PRJNA702666 2021-03-30 birds
47 live sharksucker (v1 2019) Echeneis naucrates GCF_900963305.1_fEcheNa1.1 SAMEA4966390 PRJEB31992 2019-04-11 fish
48 lumpfish (genbank) Cyclopterus lumpus GCA_009769545.1_fCycLum1.pri SAMN12629502 PRJNA562003 2019-12-23 fish
49 mute swan (2019) Cygnus olor GCA_009769625.1_bCygOlo1.pri SAMN12621369 PRJNA561960 2019-12-23 birds
50 mute swan (bCygOlo1 v1 alternate hap 2019) Cygnus olor GCA_009769485.1_bCygOlo1.alt SAMN12621369 PRJNA561961 2019-12-19 birds
51 New Zealand spotty (genbank) Notolabrus celidotus GCA_009762535.1_fNotCel1.pri SAMN12623201 PRJNA561956 2019-12-18 fish
52 northern pike Esox lucius GCA_011004845.1_fEsoLuc1.pri SAMN12623624 PRJNA561977 2020-03-05 fish
53 pale spear-nosed bat (MPI-MPIP v1 2019) Phyllostomus discolor GCF_004126475.1_mPhyDis1_v1.p SAMN09948786 PRJNA489141 2019-02-07 mammals
54 pale spear-nosed bat (alternate hap MPI-MPIP 2019) Phyllostomus discolor GCA_004115245.1_mPhyDis1_v1.h SAMN09948786 PRJNA489142 2019-01-28 mammals
55 platypus (Pmale09 v3 2020) Ornithorhynchus anatinus GCA_004115215.3_mOrnAna1.pri.v3 SAMN08537700 PRJNA489114 2020-04-13 mammals
56 prehistoric monster fish Thalassophryne amazonica GCA_902500255.1_fThaAma1.1 SAMEA104129913 PRJEB34606 2019-09-30 fish
57 reedfish (2019) Erpetoichthys calabaricus GCF_900747795.1_fErpCal1.1 SAMEA104026374 PRJEB31579 2019-03-26 fish
58 river trout (v1 2019) Salmo trutta GCF_901001165.1_fSalTru1.1 SAMEA994732 PRJEB32115 2019-06-02 fish
59 smalltooth sawfish (v2 2019 genbank) Pristis pectinata GCA_009764475.1_sPriPec2.pri SAMN12629505 PRJNA562009 2019-12-19 sharks
60 Siamese fighting fish (2019) Betta splendens GCF_900634795.2_fBetSpl5.2 SAMEA104381735 PRJEB30365 2019-03-20 fish
61 Swainson's thrush (v1 2019) Catharus ustulatus GCF_009819885.1_bCatUst1.pri SAMN12618602 PRJNA561933 2019-12-31 birds
62 Swainson's thrush (bCatUst1 v1 alternate hap 2019) Catharus ustulatus GCA_009819505.1_bCatUst1.alt SAMN12618602 PRJNA561934 2019-12-23 birds
63 thorny skate (genbank 2020) Amblyraja radiata GCA_010909765.1_sAmbRad1.pri SAMN09948523 PRJNA591369 2020-02-21 sharks
64 thorny skate (v1 2020) Amblyraja radiata GCF_010909765.1_sAmbRad1.pri SAMN09948523 PRJNA591369 2020-02-21 sharks
65 torafugu (fTakRub1.2 2019 refseq) Takifugu rubripes GCF_901000725.2_fTakRub1.2 SAMEA104384834 PRJEB31988 2019-06-05 fish
66 zebra finch (genbank 2020 Blue55 female) Taeniopygia guttata GCA_009859065.2_bTaeGut2.pri.v2 SAMN09946140 PRJNA489186 2020-04-01 birds
67 zebra finch (refseq 2019 Black17 male) Taeniopygia guttata GCF_003957565.1_bTaeGut1_v1.p SAMN02981239 PRJNA489098 2019-05-16 birds
68 zebra finch (genbank 2019 Black17 male) Taeniopygia guttata GCA_003957565.2_bTaeGut1_v1.p SAMN02981239 PRJNA489098 2019-05-16 birds
69 zebra finch (alternate hap Black17 2018) Taeniopygia guttata GCA_003957525.1_bTaeGut1_v1.h SAMN02981239 PRJNA489099 2018-12-20 birds
70 zig-zag eel (v1.2 2019 refseq) 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