VGP - Vertebrate Genomes Project assembly hub

VGP logo

This assembly hub contains assemblies released by the Vertebrate Genomes Project. (set of alternate/haplotype 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/altHub.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 Abyssinian ground-hornbill Bucorvus abyssinicus GCA_009769595.1_bBucAby1.alt SAMN12614799 PRJNA561886 2019-12-19 birds
2 American flamingo Phoenicopterus ruber ruber GCA_009819805.1_bPhoRub2.alt SAMN12614931 PRJNA561889 2019-12-23 birds
3 Anna's hummingbird Calypte anna GCA_003957575.1_bCalAnn1_v1.h SAMN02265252 PRJNA489140 2018-12-20 birds
4 Asian bonytongue Scleropages formosus GCA_900964985.2_fSclFor1.1_alternate_haplotype SAMEA4872123 PRJEB31996 2019-04-11 fish
5 Atlantic cod Gadus morhua GCA_902167395.1_gadMor3.0_alternate_haplotype SAMEA5574046 PRJEB33454 2019-07-16 fish
6 Atlantic halibut Hippoglossus hippoglossus GCA_009819745.1_fHipHip1.alt SAMN12629501 PRJNA562002 2019-12-27 fish
7 European turtle dove Streptopelia turtur GCA_901699165.1_bStrTur1.1_alternate_haplotype SAMEA994735 PRJEB32725 2019-06-02 birds
8 blackcap Sylvia atricapilla GCA_009819715.1_bSylAtr1.alt SAMN12369542 PRJNA558065 2019-12-23 birds
9 Blue whale Balaenoptera musculus GCA_008658375.1_mBalMus1_alternate SAMN12287136 PRJNA554523 2019-09-23 mammals
10 blunt-snouted clingfish Gouania willdenowi GCA_900650505.1_fGouWil2.1_alternate_haplotype SAMEA104026382 PRJEB30360 2019-02-07 fish
11 Korean giant-fin mudskipper Periophthalmus magnuspinnatus GCA_009829135.1_fPerMag1.alt SAMN12629500 PRJNA561999 2020-01-03 fish
12 channel bull blenny Cottoperca gobio GCA_900634435.1_fCotGob3.1_alternate_haplotype SAMEA104242975 PRJEB30256 2019-02-07 fish
13 prehistoric monster fish Thalassophryne amazonica GCA_902500245.1_fThaAma1.1_alternate_haplotype SAMEA104129913 PRJEB34605 2019-09-30 fish
14 tiny Cayenne caecilian Microcaecilia unicolor GCA_901765105.1_aMicUni1.1_alternate_haplotype SAMEA104387962 PRJEB32738 2019-07-08 amphibians
15 Gaboon caecilian Geotrypetes seraphini GCA_902459495.1_aGeoSer1.1_alternate_haplotype SAMEA104387963 PRJEB33991 2019-08-18 amphibians
16 California sea lion Zalophus californianus GCA_009762295.1_mZalCal1.alt SAMN12368149 PRJNA559674 2019-12-17 mammals
17 Canada lynx Lynx canadensis GCA_007474575.1_mLynCan4_v1.alt SAMN09948483 PRJNA489108 2019-07-25 mammals
18 carmine bee-eater Merops nubicus GCA_009819585.1_bMerNub1.alt SAMN12621035 PRJNA561895 2019-12-23 birds
19 climbing perch Anabas testudineus GCA_900650485.1_fAnaTes1.2_alternate_haplotype SAMEA104026376 PRJEB30391 2019-02-07 fish
20 common brushtail Trichosurus vulpecula GCA_011100645.1_mTriVul1.alt SAMN12629507 PRJNA562013 2020-03-09 mammals
21 common tern Sterna hirundo GCA_009819645.1_bSteHir1.alt SAMN12369541 PRJNA558063 2019-12-23 birds
22 common yellowthroat Geothlypis trichas GCA_009764545.1_bGeoTri1.alt SAMN12631222 PRJNA589704 2019-12-18 birds
23 denticle herring Denticeps clupeoides GCA_900700345.2_fDenClu1.1_alternate_haplotype SAMEA104129917 PRJEB31546 2019-03-27 fish
24 East African grey crowned-crane Balearica regulorum gibbericeps GCA_011004865.1_bBalReg1.alt SAMN12615749 PRJNA561891 2020-02-24 birds
25 ermine Mustela erminea GCA_009829165.1_mMusErm1.alt SAMN12611999 PRJNA561930 2020-01-03 mammals
26 Eurasian red squirrel Sciurus vulgaris GCA_902685485.1_mSciVul1.1_alternate_haplotype SAMEA994733 PRJEB35379 2019-11-26 mammals
27 European starfish Asterias rubens GCA_902459445.1_eAstRub1.2_alternate_haplotype SAMEA994741 PRJEB33973 2019-08-16 echinoderm
28 flier cichlid Archocentrus centrarchus GCA_007364235.1_fArcCen1_v1.h SAMN09948522 PRJNA489130 2019-07-24 fish
29 gilthead seabream Sparus aurata GCA_900880695.1_fSpaAur1.1_alternate_haplotype SAMEA104384835 PRJEB31902 2019-07-11 fish
30 golden eagle Aquila chrysaetos chrysaetos GCA_902153765.1_bAquChr1.2_alternate_haplotype SAMEA994725 PRJEB33298 2019-07-08 birds
31 Goodes thornscrub tortoise Gopherus evgoodei GCA_007399395.1_rGopEvg1_v1.alt SAMN03496275 PRJNA489104 2019-07-24 reptiles
32 greater horseshoe bat Rhinolophus ferrumequinum GCA_004115295.1_mRhiFer1_v1.h SAMN09948510 PRJNA489105 2019-01-28 mammals
33 greater pipefish Syngnathus acus GCA_901709685.1_fSynAcu1.1_alternate_haplotype SAMEA104381750 PRJEB32742 2019-06-02 fish
34 Indian glassy fish Parambassis ranga GCA_900651595.1_fParRan2.1_alternate_haplotype SAMEA4675621 PRJEB30258 2019-02-12 fish
35 jewelled blenny Salarias fasciatus GCA_902148835.1_fSalaFa1.1_alternate_haplotype SAMEA4966329 PRJEB33183 2019-07-03 fish
36 Kakapo Strigops habroptila GCA_004011185.1_bStrHab1_v1.h SAMN09948751 PRJNA489134 2019-01-10 birds
37 lance-tailed manakin Chiroxiphia lanceolata GCA_009829205.1_bChiLan1.alt SAMN12620979 PRJNA561944 2020-01-03 birds
38 leatherback sea turtle Dermochelys coriacea GCA_009762595.1_rDerCor1.alt SAMN12629498 PRJNA561994 2019-12-18 reptiles
39 live sharksucker Echeneis naucrates GCA_900963505.1_fEcheNa1.1_alternate_haplotype SAMEA4966390 PRJEB31993 2019-04-11 fish
40 lumpfish Cyclopterus lumpus GCA_009769515.1_fCycLum1.alt SAMN12629502 PRJNA562004 2019-12-19 fish
41 milkfish Chanos chanos GCA_902362175.1_fChaCha1.1_alternate_haplotype SAMEA5159473 PRJEB33881 2019-08-16 fish
42 mute swan Cygnus olor GCA_009769485.1_bCygOlo1.alt SAMN12621369 PRJNA561961 2019-12-19 birds
43 New Caledonian crow Corvus moneduloides GCA_009651025.1_bCorMon1.alt SAMN12368441 PRJNA560982 2019-11-12 birds
44 New Zealand spotty Notolabrus celidotus GCA_009762545.1_fNotCel1.alt SAMN12623201 PRJNA561957 2019-12-17 fish
45 northern pike Esox lucius GCA_011004835.1_fEsoLuc1.alt SAMN12623624 PRJNA561978 2020-02-24 fish
46 orbiculate cardinalfish Sphaeramia orbicularis GCA_902148825.1_fSphaOr1.1_alternate_haplotype SAMEA4966328 PRJEB33176 2019-07-03 fish
47 pale spear-nosed bat Phyllostomus discolor GCA_004115245.1_mPhyDis1_v1.h SAMN09948786 PRJNA489142 2019-01-28 mammals
48 pinecone soldierfish Myripristis murdjan GCA_902148815.1_fMyrMur1.1_alternate_haplotype SAMEA4872133 PRJEB33187 2019-07-03 fish
49 platypus Ornithorhynchus anatinus GCA_004115175.2_mOrnAna1.alt.v3 SAMN08537700 PRJNA489115 2020-04-06 mammals
50 razorbill Alca torda GCA_008658355.1_bAlcTor1_alternate SAMN12292087 PRJNA554521 2019-09-23 birds
51 red-crested turaco Tauraco erythrolophus GCA_009764505.1_bTauEry1.alt SAMN12621036 PRJNA561948 2019-12-18 birds
52 red-legged seriema Cariama cristata GCA_009819485.1_bCarCri1.alt SAMN12614807 PRJNA561893 2019-12-23 birds
53 reedfish Erpetoichthys calabaricus GCA_900700845.2_fErpCal1.1_alternate_haplotype SAMEA104026374 PRJEB31582 2019-03-27 fish
54 sand lizard Lacerta agilis GCA_009819545.1_rLacAgi1.alt SAMN12629509 PRJNA562019 2019-12-23 reptiles
55 sea lamprey Petromyzon marinus GCA_010993595.1_kPetMar1.alt SAMN12629506 PRJNA562012 2020-02-24 otherChordates
56 Siamese fighting fish Betta splendens GCA_900651605.1_fBetSpl5.1_alternate_haplotype SAMEA104381735 PRJEB30366 2019-02-07 fish
57 smalltooth sawfish Pristis pectinata GCA_009764485.1_sPriPec2.alt SAMN12629505 PRJNA562010 2019-12-18 sharks
58 Swainson's thrush Catharus ustulatus GCA_009819505.1_bCatUst1.alt SAMN12618602 PRJNA561934 2019-12-23 birds
59 thorny skate Amblyraja radiata GCA_010909745.1_sAmbRad1.alt SAMN09948523 PRJNA591368 2020-02-14 sharks
60 torafugu Takifugu rubripes GCA_901000745.3_fTakRub1.2_alternate_haplotype SAMEA104384834 PRJEB31989 2019-06-05 fish
61 tufted duck Aythya fuligula GCA_009819845.1_bAytFul2.alt SAMN12621346 PRJNA561953 2019-12-23 birds
62 two-lined caecilian Rhinatrema bivittatum GCA_901001175.1_aRhiBiv1.1_alternate_haplotype SAMEA104387956 PRJEB32112 2019-06-02 amphibians
63 vaquita Phocoena sinus GCA_008692045.1_mPhoSin1.alt SAMN12325353 PRJNA557832 2019-09-24 mammals
64 Western terrestrial garter snake Thamnophis elegans GCA_009769695.1_rThaEle1.alt SAMN12629499 PRJNA561997 2019-12-19 reptiles
65 yellow-throated sandgrouse Pterocles gutturalis GCA_009769505.1_bPteGut1.alt SAMN12623217 PRJNA561959 2019-12-19 birds
66 zebra finch Taeniopygia guttata GCA_003957525.1_bTaeGut1_v1.h SAMN02981239 PRJNA489099 2018-12-20 birds
67 zebra finch Taeniopygia guttata GCA_009859025.1_bTaeGut2.p.v1.alt SAMN09946140 PRJNA489187 2020-01-13 birds
68 zig-zag eel Mastacembelus armatus GCA_900700395.1_fMasArm1.2_alternate_haplotype SAMEA104026378 PRJEB31553 2019-04-01 fish

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