Fish Genomes assembly hubs

Assemblies from NCBI/Genbank/Refseq sources, subset of fish only.

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.
  2. Instead, you can attach the entire set of assemblies as one group to the genome browser with the following links depending upon which of our mirror site browsers you prefer to use:
  3. 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/fish/hub.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 Fish 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/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
1 Amazon molly Poecilia formosa GCF_000485575.1_Poecilia_formosa-5.1.2 SAMN02981564 PRJNA89109 2013-10-28
2 Arctic char Salvelinus alpinus GCF_002910315.2_ASM291031v2 SAMN06561764 PRJNA348349 2018-02-12
3 Asian bonytongue Scleropages formosus GCF_900964775.1_fSclFor1.1 SAMEA4872123 PRJEB31995 2019-04-11
4 Atlantic cod Gadus morhua GCF_902167405.1_gadMor3.0 SAMEA5574046 PRJEB33455 2019-07-16
5 Atlantic herring Clupea harengus GCF_900700415.1_Ch_v2.0.2 SAMEA5339254 PRJEB31270 2019-04-16
6 Atlantic salmon Salmo salar GCF_000233375.1_ICSASG_v2 SAMN02749551 PRJNA72713 2015-06-10
7 ballan wrasse Labrus bergylta GCF_900080235.1_BallGen_V1 SAMEA3939555 PRJEB13687 2016-05-03
8 barramundi perch Lates calcarifer GCF_001640805.1_ASM164080v1 SAMN04026617 PRJNA294489 2016-05-09
9 bicolor damselfish Stegastes partitus GCF_000690725.1_Stegastes_partitus-1.0.2 SAMN02743342 PRJNA89147 2014-05-13
10 black rockcod Notothenia coriiceps GCF_000735185.1_NC01 SAMN02206445 PRJNA66471 2014-07-29
11 blue tilapia Oreochromis aureus GCF_005870065.1_ASM587006v1 SAMN11513266 PRJNA539829 2019-05-28
12 blunt-snouted clingfish Gouania willdenowi GCF_900634775.1_fGouWil2.1 SAMEA104026382 PRJEB30359 2019-02-06
13 bony fishes Pundamilia nyererei GCF_000239375.1_PunNye1.0 SAMN00149614 PRJNA60367 2011-12-22
14 bony fishes Austrofundulus limnaeus GCF_001266775.1_Austrofundulus_limnaeus-1.0 SAMN03490872 PRJNA280995 2015-07-28
15 bony fishes Sinocyclocheilus anshuiensis GCF_001515605.1_SAMN03320099.WGS_v1.1 SAMN03320099 PRJNA274017 2015-12-14
16 bony fishes Sinocyclocheilus rhinocerous GCF_001515625.1_SAMN03320098_v1.1 SAMN03320098 PRJNA274017 2015-12-14
17 bony fishes Sinocyclocheilus grahami GCF_001515645.1_SAMN03320097.WGS_v1.1 SAMN03320097 PRJNA274017 2015-12-16
18 bony fishes Paramormyrops kingsleyae GCF_002872115.1_PKINGS_0.1 SAMN08000665 PRJNA417677 2018-01-10
19 bony fishes Cottoperca gobio GCF_900634415.1_fCotGob3.1 SAMEA104242975 PRJEB30248 2019-02-06
20 Burton's mouthbrooder Haplochromis burtoni GCF_000239415.1_AstBur1.0 SAMN00139641 PRJNA60363 2011-12-22
21 channel catfish Ictalurus punctatus GCF_001660625.1_IpCoco_1.2 SAMN03486842 PRJNA281269 2016-06-21
22 Chinook salmon Oncorhynchus tshawytscha GCF_002872995.1_Otsh_v1.0 SAMN07843558 PRJNA416144 2018-01-16
23 climbing perch Anabas testudineus GCF_900324465.1_fAnaTes1.1 SAMEA104026376 PRJEB25768 2018-03-31
24 clown anemonefish Amphiprion ocellaris GCF_002776465.1_AmpOce1.0 SAMN07982614 PRJNA407816 2017-11-16
25 coho salmon Oncorhynchus kisutch GCF_002021735.2_Okis_V2 SAMN05991263 PRJNA352719 2019-11-04
26 common carp Cyprinus carpio GCF_000951615.1_common_carp_genome SAMEA2757102 PRJEB7241 2014-11-03
27 denticle herring Denticeps clupeoides GCF_900700375.1_fDenClu1.1 SAMEA104129917 PRJEB31545 2019-03-16
28 eastern happy Astatotilapia calliptera GCF_900246225.1_fAstCal1.2 SAMEA104026430 PRJEB24325 2018-05-30
29 electric eel Electrophorus electricus GCF_003665695.1_Ee_SOAP_WITH_SSPACE SAMN02802636 PRJNA249073 2018-10-30
30 flier cichlid Archocentrus centrarchus GCF_007364275.1_fArcCen1 SAMN09948522 PRJNA489129 2019-08-01
31 gilthead seabream Sparus aurata GCF_900880675.1_fSpaAur1.1 SAMEA104384835 PRJEB31901 2019-07-30
32 goldfish Carassius auratus GCF_003368295.1_ASM336829v1 SAMN09670328 PRJNA481500 2018-08-09
33 great blue-spotted mudskipper Boleophthalmus pectinirostris GCF_000788275.1_BP.fa SAMN03201692 PRJNA232434 2014-12-02
34 greater amberjack Seriola dumerili GCF_002260705.1_Sdu_1.0 SAMD00083043 PRJDB5856 2017-08-03
35 guppy Poecilia reticulata GCF_000633615.1_Guppy_female_1.0_MT SAMN02404645 PRJNA238429 2014-04-28
36 Indian glassy fish Parambassis ranga GCF_900634625.1_fParRan2.1 SAMEA4675621 PRJEB30257 2019-02-06
37 Indian medaka Oryzias melastigma GCF_002922805.1_Om_v0.7.RACA SAMN07596545 PRJNA401159 2018-02-07
38 Japanese flounder Paralichthys olivaceus GCF_001970005.1_Flounder_ref_guided_V1.0 SAMN05817825 PRJNA344006 2017-01-24
39 Japanese medaka Oryzias latipes GCF_002234675.1_ASM223467v1 SAMN06689957 PRJNA325079 2017-07-27
40 jewelled blenny Salarias fasciatus GCF_902148845.1_fSalaFa1.1 SAMEA4966329 PRJEB33184 2019-07-03
41 large yellow croaker Larimichthys crocea GCF_000972845.2_L_crocea_2.0 SAMN03092871 PRJNA245366 2018-11-27
42 live sharksucker Echeneis naucrates GCF_900963305.1_fEcheNa1.1 SAMEA4966390 PRJEB31992 2019-04-11
43 lyretail cichlid Neolamprologus brichardi GCF_000239395.1_NeoBri1.0 SAMN00139653 PRJNA60365 2011-12-22
44 mangrove rivulus Kryptolebias marmoratus GCF_001649575.1_ASM164957v1 SAMN04622665 PRJNA317650 2016-05-22
45 Mexican tetra Astyanax mexicanus GCF_000372685.2_Astyanax_mexicanus-2.0 SAMN02981523 PRJNA89115 2017-09-25
46 milkfish Chanos chanos GCF_902362185.1_fChaCha1.1 SAMEA5159473 PRJEB33882 2019-08-14
47 Monterrey platyfish Xiphophorus couchianus GCF_001444195.1_X_couchianus-1.0 SAMN03922721 PRJNA290781 2018-09-19
48 mummichog Fundulus heteroclitus GCF_000826765.1_Fundulus_heteroclitus-3.0.2 SAMN03277211 PRJNA177717 2015-01-21
49 Nile tilapia Oreochromis niloticus GCF_001858045.2_O_niloticus_UMD_NMBU SAMN05859795 PRJNA344471 2018-06-29
50 northern pike Esox lucius GCF_004634155.1_Eluc_v4 SAMN09690694 PRJNA221548 2019-04-17
51 orbiculate cardinalfish Sphaeramia orbicularis GCF_902148855.1_fSphaOr1.1 SAMEA4966328 PRJEB33177 2019-07-03
52 pike-perch Sander lucioperca GCF_008315115.1_SLUC_FBN_1 SAMN12618724 PRJNA561467 2019-09-06
53 pinecone soldierfish Myripristis murdjan GCF_902150065.1_fMyrMur1.1 SAMEA4872133 PRJEB33188 2019-07-03
54 rainbow trout Oncorhynchus mykiss GCF_002163495.1_Omyk_1.0 SAMN05449231 PRJNA335610 2017-06-02
55 red-bellied piranha Pygocentrus nattereri GCF_001682695.1_Pygocentrus_nattereri-1.0.2 SAMN04522165 PRJNA301891 2016-07-12
56 river trout Salmo trutta GCF_901001165.1_fSalTru1.1 SAMEA994732 PRJEB32115 2019-06-02
57 sailfin molly Poecilia latipinna GCF_001443285.1_P_latipinna-1.0 SAMN02048973 PRJNA196862 2015-11-13
58 sheepshead minnow Cyprinodon variegatus GCF_000732505.1_C_variegatus-1.0 SAMN02736898 PRJNA89149 2015-10-01
59 shortfin molly Poecilia mexicana GCF_001443325.1_P_mexicana-1.0 SAMN02048972 PRJNA196869 2015-11-13
60 Siamese fighting fish Betta splendens GCF_900634795.2_fBetSpl5.2 SAMEA104381735 PRJEB30365 2019-03-20
61 sockeye salmon Oncorhynchus nerka GCF_006149115.1_Oner_1.0 SAMN11519041 PRJNA530256 2019-06-07
62 southern platyfish Xiphophorus maculatus GCF_002775205.1_X_maculatus-5.0-male SAMN08025980 PRJNA72525 2017-12-07
63 spiny chromis Acanthochromis polyacanthus GCF_002109545.1_ASM210954v1 SAMN06347167 PRJNA311159 2017-04-25
64 striped catfish Pangasianodon hypophthalmus GCF_003671635.1_VN_pangasius SAMN08866743 PRJNA448819 2018-10-22
65 swamp eel Monopterus albus GCF_001952655.1_M_albus_1.0 SAMN06219872 PRJNA183073 2017-01-17
66 tiger tail seahorse Hippocampus comes GCF_001891065.1_H_comes_QL1_v1 SAMN04531611 PRJNA314292 2016-12-08
67 tongue sole Cynoglossus semilaevis GCF_000523025.1_Cse_v1.0 SAMN02595200 PRJNA73987 2014-01-28
68 torafugu Takifugu rubripes GCF_901000725.2_fTakRub1.2 SAMEA104384834 PRJEB31988 2019-06-05
69 turquoise killifish Nothobranchius furzeri GCF_001465895.1_Nfu_20140520 SAMEA2698544 PRJEB5837 2015-12-11
70 wolf-eel Anarrhichthys ocellatus GCF_004355925.1_GSC_Weel_1.0 SAMN10245424 PRJNA496475 2019-03-08
71 yellow catfish Tachysurus fulvidraco GCF_003724035.1_ASM372403v1 SAMN10147840 PRJNA494039 2018-11-13
72 yellow perch Perca flavescens GCF_004354835.1_PFLA_1.0 SAMN10722690 PRJNA514308 2019-03-19
73 yellowtail amberjack Seriola lalandi dorsalis GCF_002814215.1_Sedor1 SAMN04902367 PRJNA319656 2017-12-08
74 zebra mbuna Maylandia zebra GCF_000238955.4_M_zebra_UMD2a SAMN03892560 PRJNA60369 2018-04-10
75 zebrafish Danio rerio GCF_000002035.6_GRCz11 SAMN06930106 PRJNA11776 2017-05-09
76 zig-zag eel Mastacembelus armatus GCF_900324485.1_fMasArm1.1 SAMEA104026378 PRJEB25769 2018-03-31

Additional hubs with collections of assemblies
Assembly hubs index pages:  Primates Mammals Birds Fish other vertebrates
Hubs assembly statistics:  Primates Mammals Birds Fish other vertebrates
Hubs track statistics:  Primates Mammals Birds Fish other vertebrates