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. 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/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 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 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 allis shad Alosa alosa GCF_017589495.1_AALO_Geno_1.1 SAMN16418510 PRJNA668689 2021-03-30
2 Amazon molly Poecilia formosa GCF_000485575.1_Poecilia_formosa-5.1.2 SAMN02981564 PRJNA89109 2013-10-28
3 American shad Alosa sapidissima GCF_018492685.1_fAloSap1.pri SAMN18857608 PRJNA728145 2021-05-25
4 annual killifish Austrofundulus limnaeus GCF_001266775.1_Austrofundulus_limnaeus-1.0 SAMN03490872 PRJNA280995 2015-07-28
5 Arctic char Salvelinus alpinus GCF_002910315.2_ASM291031v2 SAMN06561764 PRJNA348349 2018-02-12
6 Arkansas darter Etheostoma cragini GCF_013103735.1_CSU_Ecrag_1.0 SAMN14351042 PRJNA611833 2020-05-15
7 Asian bonytongue Scleropages formosus GCF_900964775.1_fSclFor1.1 SAMEA4872123 PRJEB31995 2019-04-11
8 Atlantic cod Gadus morhua GCF_902167405.1_gadMor3.0 SAMEA5574046 PRJEB33455 2019-07-16
9 Atlantic halibut Hippoglossus hippoglossus GCF_009819705.1_fHipHip1.pri SAMN12629501 PRJNA562001 2019-12-31
10 Atlantic herring (v2) Clupea harengus GCF_900700415.2_Ch_v2.0.2 SAMEA5339254 PRJEB31270 2019-04-16
11 Atlantic salmon (refseq 2021) Salmo salar GCF_905237065.1_Ssal_v3.1 SAMEA8062739 PRJEB43080 2021-04-21
12 Atlantic salmon (Sally 2015) Salmo salar GCF_000233375.1_ICSASG_v2 SAMN02749551 PRJNA72713 2015-06-10
13 Atlantic turbot (AOZZmale01 2020) Scophthalmus maximus GCF_013347765.1_ASM1334776v1 SAMN14896287 PRJNA631898 2020-06-18
14 ballan wrasse Labrus bergylta GCF_900080235.1_BallGen_V1 SAMEA3939555 PRJEB13687 2016-05-03
15 banded archerfish Toxotes jaculatrix GCF_017976425.1_fToxJac2.pri SAMN18445299 PRJNA717046 2021-04-15
16 barramundi perch Lates calcarifer GCF_001640805.1_ASM164080v1 SAMN04026617 PRJNA294489 2016-05-09
17 bicolor damselfish Stegastes partitus GCF_000690725.1_Stegastes_partitus-1.0.2 SAMN02743342 PRJNA89147 2014-05-13
18 black rockcod Notothenia coriiceps GCF_000735185.1_NC01 SAMN02206445 PRJNA66471 2014-07-29
19 blue tilapia (BGI-SZ) Oreochromis aureus GCF_005870065.1_ASM587006v1 SAMN11513266 PRJNA539829 2019-05-28
20 blue tilapia (Guangdong) Oreochromis aureus GCF_013358895.1_ZZ_aureus SAMN14256941 PRJNA609616 2020-06-19
21 blunt-snouted clingfish Gouania willdenowi GCF_900634775.1_fGouWil2.1 SAMEA104026382 PRJEB30359 2019-02-06
22 Boeseman's rainbowfish Melanotaenia boesemani GCF_017639745.1_fMelBoe1.pri SAMN12623618 PRJNA561965 2021-03-30
23 bony fishes Periophthalmus magnuspinnatus GCF_009829125.1_fPerMag1.pri SAMN12629500 PRJNA561998 2020-01-03
24 Burton's mouthbrooder (Broad 2011) Haplochromis burtoni GCF_000239415.1_AstBur1.0 SAMN00139641 PRJNA60363 2011-12-22
25 Burton's mouthbrooder (NCSU 2021) Haplochromis burtoni GCF_018398535.1_NCSU_Asbu1 SAMN17845830 PRJNA701062 2021-05-19
26 butterfish Scatophagus argus GCF_020382885.2_fScaArg1.pri SAMN12623616 PRJNA749579 2021-10-13
27 channel catfish (USDA103 v2 2019) Ictalurus punctatus GCF_001660625.2_IpCoco_1.2 SAMN03486842 PRJNA281269 2019-01-25
28 channel bull blenny Cottoperca gobio GCF_900634415.1_fCotGob3.1 SAMEA104242975 PRJEB30248 2019-02-06
29 chichlid (S. diagramma) Simochromis diagramma GCF_900408965.1_fSimDia1.1 SAMEA104026415 PRJEB26682 2018-06-18
30 Chinese large-mouth catfish (SWU-2019-XX 2020) Silurus meridionalis GCF_014805685.1_ASM1480568v1 SAMN14558653 PRJNA623722 2020-10-02
31 Chinook salmon (v1 2018 female) Oncorhynchus tshawytscha GCF_002872995.1_Otsh_v1.0 SAMN07843558 PRJNA416144 2018-01-16
32 Chinook salmon (v2 2021 male) Oncorhynchus tshawytscha GCF_018296145.1_Otsh_v2.0 SAMN17219827 PRJNA416144 2021-05-07
33 chum salmon Oncorhynchus keta GCF_012931545.1_Oket_V1 SAMN12367893 PRJNA556729 2020-04-29
34 climbing perch Anabas testudineus GCF_900324465.1_fAnaTes1.1 SAMEA104026376 PRJEB25768 2018-03-31
35 clown anemonefish Amphiprion ocellaris GCF_002776465.1_AmpOce1.0 SAMN07982614 PRJNA407816 2017-11-16
36 coho salmon Oncorhynchus kisutch GCF_002021735.2_Okis_V2 SAMN05991263 PRJNA352719 2019-11-04
37 common carp (2014) Cyprinus carpio GCF_000951615.1_common_carp_genome SAMEA2757102 PRJEB7241 2014-11-03
38 common carp SPL01 (2021) Cyprinus carpio GCF_018340385.1_ASM1834038v1 SAMN17005855 PRJNA682709 2021-05-12
39 copperband butterflyfish Chelmon rostratus GCF_017976325.1_fCheRos1.pri SAMN12623620 PRJNA561969 2021-04-15
40 dark-edged splitfin Girardinichthys multiradiatus GCF_021462225.1_DD_fGirMul_XY1 SAMN22242658 PRJNA768329 2022-02-24
41 delta smelt Hypomesus transpacificus GCF_021917145.1_fHypTra1 SAMN24964577 PRJNA762373 2022-02-04
42 denticle herring Denticeps clupeoides GCF_900700375.1_fDenClu1.1 SAMEA104129917 PRJEB31545 2019-03-16
43 eastern happy Astatotilapia calliptera GCF_900246225.1_fAstCal1.2 SAMEA104026430 PRJEB24325 2018-05-30
44 electric eel Electrophorus electricus GCF_003665695.1_Ee_SOAP_WITH_SSPACE SAMN02802636 PRJNA249073 2018-10-30
45 emerald rockcod Trematomus bernacchii GCF_902827165.1_fTreBer1.1 SAMEA104132834 PRJEB37642 2020-04-15
46 European perch Perca fluviatilis GCF_010015445.1_GENO_Pfluv_1.0 SAMN12071746 PRJNA549142 2020-01-30
47 fathead minnow Pimephales promelas GCF_016745375.1_EPA_FHM_2.0 SAMN12875914 PRJNA565199 2021-01-24
48 flathead mullet Mugil cephalus GCF_022458985.1_CIBA_Mcephalus_1.1 SAMN16703275 PRJNA675305 2022-03-04
49 flier cichlid Archocentrus centrarchus GCF_007364275.1_fArcCen1 SAMN09948522 PRJNA489129 2019-08-01
50 giant grouper Epinephelus lanceolatus GCF_005281545.1_ASM528154v1 SAMN10786578 PRJNA516312 2019-05-13
51 gilthead seabream Sparus aurata GCF_900880675.1_fSpaAur1.1 SAMEA104384835 PRJEB31901 2019-07-30
52 golden-line barbel Sinocyclocheilus grahami GCF_001515645.1_SAMN03320097.WGS_v1.1 SAMN03320097 PRJNA274017 2015-12-16
53 goldfish Carassius auratus GCF_003368295.1_ASM336829v1 SAMN09670328 PRJNA481500 2018-08-09
54 great blue-spotted mudskipper Boleophthalmus pectinirostris GCF_000788275.1_BP.fa SAMN03201692 PRJNA232434 2014-12-02
55 greater amberjack Seriola dumerili GCF_002260705.1_Sdu_1.0 SAMD00083043 PRJDB5856 2017-08-03
56 greater pipefish Syngnathus acus GCF_901709675.1_fSynAcu1.2 SAMEA104381750 PRJEB32741 2020-07-31
57 green swordtail Xiphophorus hellerii GCF_003331165.1_Xiphophorus_hellerii-4.1 SAMN09545741 PRJNA290782 2019-12-05
58 guppy Poecilia reticulata GCF_000633615.1_Guppy_female_1.0_MT SAMN02404645 PRJNA238429 2014-04-28
59 honeycomb rockfish Sebastes umbrosus GCF_015220745.1_fSebUmb1.pri SAMN12629503 PRJNA562005 2020-11-03
60 horned golden-line barbel Sinocyclocheilus rhinocerous GCF_001515625.1_SAMN03320098_v1.1 SAMN03320098 PRJNA274017 2015-12-14
61 humphead wrasse Cheilinus undulatus GCF_018320785.1_ASM1832078v1 SAMN14532944 PRJNA622923 2021-05-12
62 Indian medaka Oryzias melastigma GCF_002922805.2_ASM292280v2 SAMN07596545 PRJNA401159 2020-04-13
63 Indian glassy fish Parambassis ranga GCF_900634625.1_fParRan2.1 SAMEA4675621 PRJEB30257 2019-02-06
64 Japanese flounder Paralichthys olivaceus GCF_001970005.1_Flounder_ref_guided_V1.0 SAMN05817825 PRJNA344006 2017-01-24
65 Japanese medaka Oryzias latipes GCF_002234675.1_ASM223467v1 SAMN06689957 PRJNA325079 2017-07-27
66 jewelled blenny Salarias fasciatus GCF_902148845.1_fSalaFa1.1 SAMEA4966329 PRJEB33184 2019-07-03
67 lake trout Salvelinus namaycush GCF_016432855.1_SaNama_1.0 SAMN16985724 PRJNA682269 2021-01-06
68 lake whitefish (EN20210322 male 2021 Laval U) Coregonus clupeaformis GCF_018398675.1_ASM1839867v1 SAMN18351024 PRJNA715481 2021-05-25
69 lake whitefish (EN_2021a female 2021 Laval U) Coregonus clupeaformis GCF_020615455.1_ASM2061545v1 SAMN21920801 PRJNA767633 2021-11-04
70 large yellow croaker Larimichthys crocea GCF_000972845.2_L_crocea_2.0 SAMN03092871 PRJNA245366 2018-11-27
71 largemouth bass Micropterus salmoides GCF_014851395.1_ASM1485139v1 SAMN15299117 PRJNA640112 2020-10-05
72 leopard coralgrouper Plectropomus leopardus GCF_008729295.1_YSFRI_Pleo_2.0 SAMN11897347 PRJNA545594 2020-05-27
73 live sharksucker Echeneis naucrates GCF_900963305.1_fEcheNa1.1 SAMEA4966390 PRJEB31992 2019-04-11
74 lumpfish Cyclopterus lumpus GCF_009769545.1_fCycLum1.pri SAMN12629502 PRJNA562003 2019-12-23
75 lyretail cichlid Neolamprologus brichardi GCF_000239395.1_NeoBri1.0 SAMN00139653 PRJNA60365 2011-12-22
76 mandarin fish Siniperca chuatsi GCF_020085105.1_ASM2008510v1 SAMN19768590 PRJNA738969 2021-09-24
77 mangrove rivulus Kryptolebias marmoratus GCF_001649575.2_ASM164957v2 SAMN04622665 PRJNA626665 2020-11-16
78 Mexican tetra (2017 WashU) Astyanax mexicanus GCF_000372685.2_Astyanax_mexicanus-2.0 SAMN02981523 PRJNA89115 2017-09-25
79 Mexican tetra (Pach_M1 Pachon cave 2021) Astyanax mexicanus GCA_019721115.1_AMEX_1.1 SAMN18310656 PRJNA734455 2021-08-25
80 milkfish Chanos chanos GCF_902362185.1_fChaCha1.1 SAMEA5159473 PRJEB33882 2019-08-14
81 Monterrey platyfish Xiphophorus couchianus GCF_001444195.1_X_couchianus-1.0 SAMN03922721 PRJNA290781 2018-09-19
82 mummichog (Maine) Fundulus heteroclitus GCF_000826765.1_Fundulus_heteroclitus-3.0.2 SAMN03277211 PRJNA177717 2015-01-21
83 mummichog (U. Missouri) Fundulus heteroclitus GCF_011125445.2_MU-UCD_Fhet_4.1 SAMN13668183 PRJNA597160 2020-08-13
84 Nile tilapia Oreochromis niloticus GCF_001858045.2_O_niloticus_UMD_NMBU SAMN05859795 PRJNA344471 2018-06-29
85 ninespine stickleback Pungitius pungitius GCF_902500615.1_NSP_V7 SAMEA5986199 PRJEB33823 2020-10-12
86 northern pike Esox lucius GCF_004634155.1_Eluc_v4 SAMN09690694 PRJNA221548 2019-04-17
87 Old Calabar mormyrid Paramormyrops kingsleyae GCF_002872115.1_PKINGS_0.1 SAMN08000665 PRJNA417677 2018-01-10
88 orangethroat darter Etheostoma spectabile GCF_008692095.1_UIUC_Espe_1.0 SAMN12373147 PRJNA556880 2019-10-07
89 orbiculate cardinalfish Sphaeramia orbicularis GCF_902148855.1_fSphaOr1.1 SAMEA4966328 PRJEB33177 2019-07-03
90 P.nyererei 1_Seehausen Pundamilia nyererei GCF_000239375.1_PunNye1.0 SAMN00149614 PRJNA60367 2011-12-22
91 Pacific halibut (PH-IPHC-18 2020) Hippoglossus stenolepis GCF_013339905.1_IPHC_HiSten_1.0 SAMN14503176 PRJNA622249 2020-06-16
92 Pacific halibut (QCI-W04-F060 2022) Hippoglossus stenolepis GCF_022539355.2_HSTE1.2 SAMN25516224 PRJNA622249 2022-03-10
93 pike-perch Sander lucioperca GCF_008315115.2_SLUC_FBN_1.2 SAMN12618724 PRJNA561467 2020-08-14
94 pinecone soldierfish Myripristis murdjan GCF_902150065.1_fMyrMur1.1 SAMEA4872133 PRJEB33188 2019-07-03
95 pink salmon Oncorhynchus gorbuscha GCF_021184085.1_OgorEven_v1.0 SAMN18987060 PRJNA556728 2021-12-15
96 ploughfish Gymnodraco acuticeps GCF_902827175.1_fGymAcu1.1 SAMEA104242997 PRJEB37639 2020-04-15
97 prehistoric monster fish Thalassophryne amazonica GCF_902500255.1_fThaAma1.1 SAMEA104129913 PRJEB34606 2019-09-30
98 rainbow trout (Swanson) Oncorhynchus mykiss GCF_002163495.1_Omyk_1.0 SAMN05449231 PRJNA335610 2017-06-02
99 rainbow trout (Arlee) Oncorhynchus mykiss GCF_013265735.2_USDA_OmykA_1.1 SAMN14537335 PRJNA623027 2020-09-23
100 red-bellied piranha Pygocentrus nattereri GCF_001682695.1_Pygocentrus_nattereri-1.0.2 SAMN04522165 PRJNA301891 2016-07-12
101 Rio pearlfish (Nwh7 v2 2021) Nematolebias whitei GCF_014905685.2_NemWhi1 SAMN12588121 PRJNA560526 2021-03-24
102 river trout Salmo trutta GCF_901001165.1_fSalTru1.1 SAMEA994732 PRJEB32115 2019-06-02
103 sailfin molly Poecilia latipinna GCF_001443285.1_P_latipinna-1.0 SAMN02048973 PRJNA196862 2015-11-13
104 Senegalese sole Solea senegalensis GCF_019176455.1_IFAPA_SoseM_1 SAMN15430148 PRJNA643826 2021-07-09
105 sheepshead minnow Cyprinodon variegatus GCF_000732505.1_C_variegatus-1.0 SAMN02736898 PRJNA89149 2015-10-01
106 shortfin molly Poecilia mexicana GCF_001443325.1_P_mexicana-1.0 SAMN02048972 PRJNA196869 2015-11-13
107 Siamese fighting fish (v3 2020) Betta splendens GCF_900634795.3_fBetSpl5.3 SAMEA104381735 PRJEB30365 2020-08-25
108 smallmouth bass Micropterus dolomieu GCF_021292245.1_ASM2129224v1 SAMN22851699 PRJNA777359 2022-01-11
109 sockeye salmon (On170113-E2 v2 2019) Oncorhynchus nerka GCF_006149115.2_Oner_1.1 SAMN11519041 PRJNA530256 2019-06-07
110 South Georgia icefish Pseudochaenichthys georgianus GCF_902827115.1_fPseGeo1.1 SAMEA104132832 PRJEB37648 2020-04-15
111 southern platyfish Xiphophorus maculatus GCF_002775205.1_X_maculatus-5.0-male SAMN08025980 PRJNA72525 2017-12-07
112 southern bluefin tuna Thunnus maccoyii GCF_910596095.1_fThuMac1.1 SAMEA8654747 PRJEB46021 2021-07-07
113 Southwestern China cavefish Sinocyclocheilus anshuiensis GCF_001515605.1_SAMN03320099.WGS_v1.1 SAMN03320099 PRJNA274017 2015-12-14
114 spiny chromis Acanthochromis polyacanthus GCF_002109545.1_ASM210954v1 SAMN06347167 PRJNA311159 2017-04-25
115 striped catfish Vietnam Pangasianodon hypophthalmus GCF_003671635.1_VN_pangasius SAMN08866743 PRJNA448819 2018-10-22
116 striped sea-bass Morone saxatilis GCF_004916995.1_NCSU_SB_2.0 SAMN11399929 PRJNA532441 2019-04-26
117 striped catfish Indonesia Pangasianodon hypophthalmus GCF_009078355.1_GENO_Phyp_1.0 SAMN11969507 PRJNA547555 2019-10-22
118 Sumatra barb Puntigrus tetrazona GCF_018831695.1_ASM1883169v1 SAMN17036344 PRJNA683758 2021-06-10
119 swamp eel Monopterus albus GCF_001952655.1_M_albus_1.0 SAMN06219872 PRJNA183073 2017-01-17
120 swordfish Xiphias gladius GCF_016859285.1_ASM1685928v1 SAMN16522248 PRJNA670841 2021-02-12
121 tambaqui Colossoma macropomum GCF_904425465.1_Colossoma_macropomum SAMEA7302664 PRJEB40318 2020-09-25
122 three-spined stickleback Gasterosteus aculeatus aculeatus GCF_016920845.1_GAculeatus_UGA_version5 SAMN15223905 PRJNA639125 2021-02-23
123 tiger tail seahorse (QL1 v2 2016) Hippocampus comes GCF_001891065.2_H_comes_QL1_v1.1 SAMN04531611 PRJNA314292 2016-12-08
124 tongue sole Cynoglossus semilaevis GCF_000523025.1_Cse_v1.0 SAMN02595200 PRJNA73987 2014-01-28
125 torafugu Takifugu rubripes GCF_901000725.2_fTakRub1.2 SAMEA104384834 PRJEB31988 2019-06-05
126 turbot (ysfricsl-2021 2022) Scophthalmus maximus GCF_022379125.1_ASM2237912v1 SAMN24450573 PRJNA792617 2022-02-24
127 turquoise killifish Nothobranchius furzeri GCF_001465895.1_Nfu_20140520 SAMEA2698544 PRJEB5837 2015-12-11
128 western mosquitofish Gambusia affinis GCF_019740435.1_SWU_Gaff_1.0 SAMN13752108 PRJNA599452 2021-08-25
129 White Sands pupfish Cyprinodon tularosa GCF_016077235.1_ASM1607723v1 SAMN16509697 PRJNA670474 2020-12-15
130 wolf-eel Anarrhichthys ocellatus GCF_004355925.1_GSC_Weel_1.0 SAMN10245424 PRJNA496475 2019-03-08
131 Wuchang bream Megalobrama amblycephala GCF_018812025.1_ASM1881202v1 SAMN18522313 PRJNA343584 2021-06-09
132 yellow catfish (hzauxx_2018 2022) Tachysurus fulvidraco GCF_022655615.1_HZAU_PFXX_2.0 SAMN10031298 PRJNA489116 2022-03-21
133 yellow catfish (Tf-2017 2018) Tachysurus fulvidraco GCF_003724035.1_ASM372403v1 SAMN10147840 PRJNA494039 2018-11-13
134 yellow perch (YP-PL-M2 2019) Perca flavescens GCF_004354835.1_PFLA_1.0 SAMN10722690 PRJNA514308 2019-03-19
135 yellowfin seabream Acanthopagrus latus GCF_904848185.1_fAcaLat1.1 SAMN16236878 PRJEB40700 2020-10-12
136 yellowfin tuna Thunnus albacares GCF_914725855.1_fThuAlb1.1 SAMEA8654749 PRJEB47267 2021-09-16
137 yellowtail amberjack Seriola lalandi dorsalis GCF_002814215.1_Sedor1 SAMN04902367 PRJNA319656 2017-12-08
138 Zealand spotty Notolabrus celidotus GCF_009762535.1_fNotCel1.pri SAMN12623201 PRJNA561956 2019-12-18
139 zebra mbuna Maylandia zebra GCF_000238955.4_M_zebra_UMD2a SAMN03892560 PRJNA60369 2018-04-10
140 zebrafish T5D Danio rerio GCA_018400075.1_ASM1840007v1 SAMN09710566 PRJNA482650 2021-05-19
141 zebrafish GRCz11 Danio rerio GCF_000002035.6_GRCz11 SAMN06930106 PRJNA11776 2017-05-09
142 zig-zag eel Mastacembelus armatus GCF_900324485.1_fMasArm1.1 SAMEA104026378 PRJEB25769 2018-03-31

Additional hubs with collections of assemblies
Collection Hub index pages: Assembly statistics: Track statistics:
Primates 52 assemblies assembly stats track stats
Mammals 301 assemblies assembly stats track stats
Birds 123 assemblies assembly stats track stats
Fishes 142 assemblies assembly stats track stats
other vertebrates 48 assemblies assembly stats track stats
Invertebrates 400 assemblies assembly stats track stats
Plants 146 assemblies assembly stats track stats
Fungi 416 assemblies assembly stats track stats
VGP - Vertebrate Genome Project 233 assemblies assembly stats track stats
legacy/superseded 136 assemblies assembly stats track stats