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 (set of legacy/superseded assemblies)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-test.gi.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-test.gi.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.


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 BioSampleBioProject assembly date,
source link
class
VGP link
1 African grass rat 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 blue whale Balaenoptera musculus GCA_009873245.2_mBalMus1.v2 SAMN12287136 PRJNA554522 2020-02-03 mammals
5 blunt-snouted clingfish Gouania willdenowi GCA_900634775.1_fGouWil2.1 SAMEA104026382 PRJEB30359 2019-02-06 fish
6 budgerigar Melopsittacus undulatus GCA_012275295.1_bMelUnd1.mat.Z SAMN12623090 PRJNA612327 2020-04-13 birds
7 California sea lion Zalophus californianus GCA_009762305.1_mZalCal1.pri SAMN12368149 PRJNA559673 2019-12-18 mammals
8 Canada lynx Lynx canadensis GCF_007474595.1_mLynCan4_v1.p SAMN09948483 PRJNA489107 2019-07-26 mammals
9 channel bull blenny Cottoperca gobio GCA_900634415.1_fCotGob3.1 SAMEA104242975 PRJEB30248 2019-02-06 fish
10 climbing perch Anabas testudineus GCA_900324465.2_fAnaTes1.2 SAMEA104026376 PRJEB25768 2018-12-19 fish
11 common brushtail Trichosurus vulpecula GCA_011100635.1_mTriVul1.pri SAMN12629507 PRJNA562014 2020-03-10 mammals
12 common bottlenose dolphin Tursiops truncatus GCA_011762595.1_mTurTru1.mat.Y SAMN12326775 PRJNA608726 2020-03-27 mammals
13 Eurasian water vole (2020) Arvicola amphibius GCF_903992535.1_mArvAmp1.1 SAMEA994740 PRJEB39550 2020-08-06 mammals
14 European turtle dove (v1.1 2019 VGP) Streptopelia turtur GCA_901699155.1_bStrTur1.1 SAMEA994735 PRJEB32724 2019-06-05 birds
15 flier cichlid Archocentrus centrarchus GCA_007364275.2_fArcCen1 SAMN09948522 PRJNA489129 2019-08-01 fish
16 Gabon caecilian Geotrypetes seraphini GCA_902459505.1_aGeoSer1.1 SAMEA104387963 PRJEB33992 2019-08-18 amphibians
17 golden eagle (2019) Aquila chrysaetos chrysaetos GCF_900496995.1_bAquChr1.2 SAMEA994725 PRJEB27699 2019-07-08 birds
18 greater horseshoe bat Rhinolophus ferrumequinum GCF_004115265.1_mRhiFer1_v1.p SAMN09948510 PRJNA489106 2019-05-16 mammals
19 greater pipefish Syngnathus acus GCA_901709675.1_fSynAcu1.1 SAMEA104381750 PRJEB32741 2019-05-29 fish
20 green sea turtle (v1 2020) Chelonia mydas GCF_015237465.1_rCheMyd1.pri SAMN12612360 PRJNA561941 2020-11-05 reptiles
21 kakapo Strigops habroptila GCA_004027225.2_bStrHab1.2.pri SAMN09948751 PRJNA489135 2020-03-04 birds
22 Korean giant-fin mudskipper (genbank) Periophthalmus magnuspinnatus GCA_009829125.1_fPerMag1.pri SAMN12629500 PRJNA561998 2020-01-03 fish
23 leatherback sea turtle (v1 2019 genbank G10K VGP) Dermochelys coriacea GCA_009764565.1_rDerCor1.pri SAMN12629498 PRJNA561993 2019-12-19 reptiles
24 leatherback sea turtle (v3 2020 refseq G10K VGP) Dermochelys coriacea GCF_009764565.2_rDerCor1.pri.v3 SAMN12629498 PRJNA561993 2020-12-09 reptiles
25 lumpfish (genbank) Cyclopterus lumpus GCA_009769545.1_fCycLum1.pri SAMN12629502 PRJNA562003 2019-12-23 fish
26 mute swan (2019) Cygnus olor GCA_009769625.1_bCygOlo1.pri SAMN12621369 PRJNA561960 2019-12-23 birds
27 New Zealand spotty (genbank) Notolabrus celidotus GCA_009762535.1_fNotCel1.pri SAMN12623201 PRJNA561956 2019-12-18 fish
28 northern pike Esox lucius GCA_011004845.1_fEsoLuc1.pri SAMN12623624 PRJNA561977 2020-03-05 fish
29 pale spear-nosed bat Phyllostomus discolor GCF_004126475.1_mPhyDis1_v1.p SAMN09948786 PRJNA489141 2019-02-07 mammals
30 platypus (v3 2020) Ornithorhynchus anatinus GCA_004115215.3_mOrnAna1.pri.v3 SAMN08537700 PRJNA489114 2020-04-13 mammals
31 prehistoric monster fish Thalassophryne amazonica GCA_902500255.1_fThaAma1.1 SAMEA104129913 PRJEB34606 2019-09-30 fish
32 Siamese fighting fish (2019) Betta splendens GCF_900634795.2_fBetSpl5.2 SAMEA104381735 PRJEB30365 2019-03-20 fish
33 Swainson's thrush (v1 2019 VGP) Catharus ustulatus GCF_009819885.1_bCatUst1.pri SAMN12618602 PRJNA561933 2019-12-31 birds
34 thorny skate (genbank 2020) Amblyraja radiata GCA_010909765.1_sAmbRad1.pri SAMN09948523 PRJNA591369 2020-02-21 sharks
35 thorny skate (v1 2020) Amblyraja radiata GCF_010909765.1_sAmbRad1.pri SAMN09948523 PRJNA591369 2020-02-21 sharks
36 zebra finch (genbank 2020 Blue55 female) Taeniopygia guttata GCA_009859065.2_bTaeGut2.pri.v2 SAMN09946140 PRJNA489186 2020-04-01 birds
37 zebra finch (refseq 2019 Black17 male) Taeniopygia guttata GCF_003957565.1_bTaeGut1_v1.p SAMN02981239 PRJNA489098 2019-05-16 birds
38 zebra finch (genbank 2019 Black17 male) Taeniopygia guttata GCA_003957565.2_bTaeGut1_v1.p SAMN02981239 PRJNA489098 2019-05-16 birds

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