VGP - Vertebrate Genomes Project assembly hub

VGP logo

This assembly hub contains assemblies released by the Vertebrate Genomes Project. (set of trio assemblies, maternal/paternal)

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/trioHub.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_011750645.1_mArvNil1.mat SAMN12611849 PRJNA561936 2020-03-25 mammals
2 African grass rat Arvicanthis niloticus GCA_011762505.1_mArvNil1.pat.X SAMN12611849 PRJNA608735 2020-03-27 mammals
3 African grass rat Arvicanthis niloticus GCA_011762545.1_mArvNil1.pat SAMN12611849 PRJNA561935 2020-03-25 mammals
4 budgerigar Melopsittacus undulatus GCA_012275265.1_bMelUnd1.mat SAMN12623090 PRJNA561964 2020-04-13 birds
5 budgerigar Melopsittacus undulatus GCA_012275275.1_bMelUnd1.pat SAMN12623090 PRJNA561963 2020-04-13 birds
6 budgerigar Melopsittacus undulatus GCA_012275295.1_bMelUnd1.mat.Z SAMN12623090 PRJNA612327 2020-04-13 birds
7 common bottlenose dolphin Tursiops truncatus GCA_011762515.1_mTurTru1.pat SAMN12326775 PRJNA561884 2020-03-25 mammals
8 common bottlenose dolphin Tursiops truncatus GCA_011762535.1_mTurTru1.mat SAMN12326775 PRJNA561885 2020-03-25 mammals
9 common bottlenose dolphin Tursiops truncatus GCF_011762595.1_mTurTru1.mat.Y SAMN12326775 PRJNA608726 2020-03-27 mammals
10 sterlet Acipenser ruthenus GCA_902713425.1_fAciRut3.1_maternal_haplotype SAMEA5572864 PRJEB35912 2020-01-08 fish
11 sterlet Acipenser ruthenus GCA_902713435.1_fAciRut3.1_paternal_haplotype SAMEA5572864 PRJEB35913 2020-01-08 fish
12 white-tufted-ear marmoset Callithrix jacchus GCA_011078405.1_mCalJac1.mat SAMN12368443 PRJNA558086 2020-03-10 primates
13 white-tufted-ear marmoset Callithrix jacchus GCA_011100535.1_mCalJac1.pat SAMN12368443 PRJNA558087 2020-03-10 primates
14 white-tufted-ear marmoset Callithrix jacchus GCA_011100555.1_mCalJac1.pat.X SAMN12368443 PRJNA597600 2020-03-10 primates
15 zebra finch Taeniopygia guttata GCA_008822115.3_bTaeGut2.mat.v3 SAMN09946140 PRJNA489100 2020-02-21 birds
16 zebra finch Taeniopygia guttata GCA_008822125.1_bTaeGut2pat SAMN09946140 PRJNA489101 2019-10-03 birds
17 zebra finch Taeniopygia guttata GCF_008822105.2_bTaeGut2.pat.W.v2 SAMN09946140 PRJNA555095 2020-02-12 birds

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