VGP - Vertebrate Genomes Project assembly hub

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 (set of legacy/superseded assemblies)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 statistics, track statistics <== additional information for these assemblies.

Listings:

  (from RepeatModeler masking)

• families fasta.gz list of URLs for the custom library created by the RepeatModeler run
• assembly 2bit file list of URLs as masked with the RepeatModeler + TRF/simpleRepeats with period of 12 or less
• the rmod.log files from each RepeatModeler run
• default GenArk 2bit file list of URLs as masked with the ordinary RepeatMasker + TRF/simpleRepeats with period of 12 or less
• this data table in tab-separated file text format (including TBD not working yet, or in VGP collection but not on the alignment list)

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 assemblies					NCBI 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