Birds Genomes assembly hubs

Assemblies from NCBI/Genbank/Refseq sources, subset of birds 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/birds/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 Birds 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 Adelie penguin Pygoscelis adeliae GCF_000699105.1_ASM69910v1 SAMN02596601 PRJNA235983 2014-06-06
2 African ostrich Struthio camelus australis GCF_000698965.1_ASM69896v1 SAMN02316164 PRJNA212875 2014-06-06
3 American crow Corvus brachyrhynchos GCF_000691975.1_ASM69197v1 SAMN02297499 PRJNA212869 2014-06-02
4 Anna's hummingbird Calypte anna GCF_003957555.1_bCalAnn1_v1.p SAMN02265252 PRJNA489139 2019-05-16
5 bald eagle Haliaeetus leucocephalus GCF_000737465.1_Haliaeetus_leucocephalus-4.0 SAMN02664716 PRJNA237821 2014-08-04
6 bar-tailed trogon Apaloderma vittatum GCF_000703405.1_ASM70340v1 SAMN02318033 PRJNA212878 2014-06-16
7 barn owl (U. Lausanne 2021) Tyto alba GCF_018691265.1_T.alba_DEE_v4.0 SAMN17526497 PRJNA694551 2021-06-03
8 barn swallow (genbank 2021) Hirundo rustica GCA_015227805.2_bHirRus1.pri.v2 SAMN14675488 PRJNA636192 2021-03-02
9 barn swallow (refseq 2021) Hirundo rustica GCF_015227805.1_bHirRus1.pri.v2 SAMN14675488 PRJNA636192 2021-03-02
10 Bengalese finch Lonchura striata domestica GCF_005870125.1_lonStrDom2 SAMN11521339 PRJNA369279 2019-06-05
11 black swan Cygnus atratus GCF_013377495.1_Cygnus_atratus_primary_v1.0 SAMN15332785 PRJNA640810 2020-06-30
12 black-throated flowerpiercer Diglossa brunneiventris GCA_019023105.1_LSU_DiBr_2.0 SAMN17308174 PRJNA629984 2021-06-24
13 blue tit Cyanistes caeruleus GCF_002901205.1_cyaCae2 SAMN03734925 PRJNA284903 2018-01-26
14 blue-crowned manakin Lepidothrix coronata GCF_001604755.1_Lepidothrix_coronata-1.0 SAMN04274560 PRJNA300662 2016-03-31
15 brown eared-pheasant Crossoptilon mantchuricum GCA_019593555.1_cma1 SAMN15899056 PRJNA659158 2021-08-13
16 brown headed cowbird Molothrus ater GCF_012460135.1_BPBGC_Mater_1.0 SAMN14074414 PRJNA606972 2020-04-20
17 brown kiwi Apteryx mantelli mantelli GCF_001039765.1_AptMant0 SAMEA2560515 PRJEB6383 2015-06-21
18 brown roatelo Mesitornis unicolor GCF_000695765.1_ASM69576v1 SAMN02339298 PRJNA212899 2014-06-02
19 budgerigar Melopsittacus undulatus GCF_000238935.1_Melopsittacus_undulatus_6.3 SAMN02981360 PRJNA72527 2012-01-02
20 burrowing owl Athene cunicularia GCF_003259725.1_athCun1 SAMN08961563 PRJNA431202 2018-06-21
21 California condor Gymnogyps californianus GCA_018139145.1_ASM1813914v1 SAMN18477433 PRJNA718609 2021-04-25
22 carmine bee-eater Merops nubicus GCF_000691845.1_ASM69184v1 SAMN02338310 PRJNA212898 2014-05-16
23 chicken Gallus gallus GCF_000002315.6_GRCg6a SAMN02981218 PRJNA13342 2018-03-27
24 Chilean tinamou Nothoprocta perdicaria GCF_003342845.1_notPer1 SAMN08476459 PRJNA433110 2018-07-26
25 chimney swift Chaetura pelagica GCF_000747805.1_ChaPel_1.0 SAMN03018471 PRJNA210808 2014-09-04
26 chuck-will's-widow (BGI_N321 v2 2014) Antrostomus carolinensis GCF_000700745.2_ASM70074v2 SAMN02318612 PRJNA212888 2014-06-10
27 collared flycatcher Ficedula albicollis GCF_000247815.1_FicAlb1.5 SAMN02981387 PRJNA75089 2013-06-27
28 common canary Serinus canaria GCF_007115625.1_cibio_Scana_2019 SAMN12017177 PRJNA548289 2019-07-18
29 common cuckoo (VGP 2021) Cuculus canorus GCA_017976375.1_bCucCan1.pri SAMN12629508 PRJNA562015 2021-04-15
30 common starling Sturnus vulgaris GCF_001447265.1_Sturnus_vulgaris-1.0 SAMN04029017 PRJNA293892 2015-11-20
31 common swift Apus apus GCA_020740795.1_bApuApu2.pri.cur SAMN22785356 PRJNA776336 2021-11-04
32 crested ibis Nipponia nippon GCF_000708225.1_ASM70822v1 SAMN02596464 PRJNA232572 2014-06-16
33 cuckoo roller Leptosomus discolor GCF_000691785.1_ASM69178v1 SAMN02333687 PRJNA212897 2014-05-23
34 Dalmatian pelican Pelecanus crispus GCF_000687375.1_ASM68737v1 SAMN02339887 PRJNA212901 2014-05-09
35 downy woodpecker (VGP 2020) Dryobates pubescens GCA_014839835.1_bDryPub1.pri SAMN12629497 PRJNA561991 2020-10-02
36 East African grey crowned-crane Balearica regulorum gibbericeps GCF_000709895.1_ASM70989v1 SAMN02318095 PRJNA212879 2014-06-25
37 emperor penguin Aptenodytes forsteri GCF_000699145.1_ASM69914v1 SAMN02596600 PRJNA235982 2014-06-06
38 emu (2018) Dromaius novaehollandiae GCF_003342905.1_droNov1 SAMN08476457 PRJNA433110 2018-07-26
39 emu (2020) Dromaius novaehollandiae GCA_016128335.1_ZJU1.0 SAMN15183959 PRJNA638233 2020-12-20
40 Eurasian nightjar Caprimulgus europaeus GCA_907165065.1_bCapEur3.1 SAMEA7524394 PRJEB44540 2021-05-17
41 Eurasian tree sparrow Passer montanus GCF_014805655.1_ASM1480565v1 SAMN07998528 PRJNA417520 2020-09-30
42 European golden plover Pluvialis apricaria GCA_017639485.1_bPluApr1.pri SAMN18353970 PRJNA715924 2021-03-30
43 European robin Erithacus rubecula GCA_903797595.2_bEriRub2.2 SAMEA4760689 PRJEB38658 2021-05-03
44 European turtle dove Streptopelia turtur GCA_901699155.2_bStrTur1.2 SAMEA994735 PRJEB32724 2021-05-17
45 garden warbler Sylvia borin GCA_014839755.1_bSylBor1.pri SAMN12618613 PRJNA561945 2020-10-02
46 golden-collared manakin Manacus vitellinus GCF_001715985.3_ASM171598v3 SAMN02299332 PRJNA335611 2019-07-03
47 golden eagle Aquila chrysaetos chrysaetos GCF_900496995.4_bAquChr1.4 SAMEA994725 PRJEB27699 2021-03-26
48 golden pheasant Chrysolophus pictus GCA_003413605.1_Chrysolophus_pictus_GenomeV1.0 SAMN02980944 PRJNA257945 2018-08-20
49 great cormorant Phalacrocorax carbo GCF_000708925.1_ASM70892v1 SAMN02339889 PRJNA212903 2014-06-17
50 great potoo Nyctibius grandis GCA_013368605.1_bNycGra1.pri SAMN12622411 PRJNA562020 2020-06-23
51 great tit Parus major GCF_001522545.3_Parus_major1.1 SAMN03083587 PRJNA208335 2019-01-15
52 greater prairie chicken Tympanuchus cupido pinnatus GCA_001870855.1_T_cupido_pinnatus_GPC_3440_v1 SAMN05433571 PRJNA330991 2016-11-07
53 greater rhea Rhea americana GCA_003343005.1_rheAme1 SAMN08476460 PRJNA433110 2018-07-26
54 greater sage-grouse Centrocercus urophasianus GCF_019232065.1_USGS_Curo_1.0 SAMN20124253 PRJNA734947 2021-07-15
55 green peafowl Pavo muticus GCA_016647715.1_ASM1664771v1 SAMN15486085 PRJNA644939 2021-01-15
56 Hawaiian crow (VGP 2021 refseq) Corvus hawaiiensis GCF_020740725.1_bCorHaw1.pri.cur SAMN22550278 PRJNA774314 2021-11-04
57 helmeted guineafowl Numida meleagris GCF_002078875.1_NumMel1.0 SAMN05969731 PRJNA352321 2017-06-01
58 hoatzin Opisthocomus hoazin GCF_000692075.1_ASM69207v1 SAMN02302474 PRJNA212873 2014-05-19
59 hooded crow (2021) Corvus cornix cornix GCF_000738735.5_ASM73873v5 SAMN02143031 PRJNA192205 2021-02-04
60 jackdaw Coloeus monedula GCA_013407035.1_ASM1340703v1 SAMN14646012 PRJNA626609 2020-07-13
61 Japanese quail Coturnix japonica GCF_001577835.2_Coturnix_japonica_2.1 SAMN03989050 PRJNA292031 2016-03-01
62 kakapo Strigops habroptila GCF_004027225.1_bStrHab1_v1.p SAMN09948751 PRJNA489135 2019-01-18
63 kea Nestor notabilis GCF_000696875.1_ASM69687v1 SAMN02339299 PRJNA212900 2014-06-05
64 killdeer Charadrius vociferus GCF_000708025.1_ASM70802v2 SAMN02296710 PRJNA212867 2014-08-05
65 lesser kestrel Falco naumanni GCF_017639655.2_bFalNau1.pat SAMN16870685 PRJNA702666 2021-03-30
66 lesser rhea Rhea pennata GCA_003342835.1_rhePen1 SAMN08476461 PRJNA433110 2018-07-26
67 little egret Egretta garzetta GCF_000687185.1_ASM68718v1 SAMN02596466 PRJNA232959 2014-05-09
68 Macqueen's bustard Chlamydotis macqueenii GCF_000695195.1_ASM69519v1 SAMN02324157 PRJNA212891 2014-06-02
69 maguari stor Ciconia maguari GCA_017639555.1_bCicMag1.pri SAMN18353822 PRJNA715733 2021-03-30
70 mallard CAU_Wild1.0 Anas platyrhynchos GCA_008746955.1_CAU_Wild1.0 SAMN12287667 PRJNA554956 2019-10-07
71 mallard PBH1.5 Anas platyrhynchos GCF_003850225.1_IASCAAS_PekingDuck_PBH1.5 SAMN10245527 PRJNA496533 2018-11-29
72 mallard ZJU1.0 Anas platyrhynchos GCF_015476345.1_ZJU1.0 SAMN15588841 PRJNA636121 2020-11-23
73 Mariana crow Corvus kubaryi GCF_017639235.1_C.kubaryi_AGA036_p1.0 SAMN16883221 PRJNA680658 2021-03-30
74 medium ground-finch Geospiza fortis GCF_000277835.1_GeoFor_1.0 SAMN00839579 PRJNA156703 2012-07-25
75 monk parakeet Myiopsitta monachus GCA_017639245.1_MMon_1.0 SAMN16846069 PRJNA679636 2021-03-30
76 mute swan Cygnus olor GCF_009769625.2_bCygOlo1.pri.v2 SAMN12621369 PRJNA561960 2021-03-31
77 northern bobwhite Colinus virginianus GCA_008692595.2_Cv_LA_2.0 SAMN09044008 PRJNA454855 2021-04-29
78 northern fulmar Fulmarus glacialis GCF_000690835.1_ASM69083v1 SAMN02324803 PRJNA212894 2014-05-13
79 Okarito brown kiwi Apteryx rowi GCF_003343035.1_aptRow1 SAMN08476454 PRJNA433110 2018-07-26
80 peregrine falcon Falco peregrinus GCF_000337955.1_F_peregrinus_v1.0 SAMN02981425 PRJNA159791 2013-02-05
81 plumbeous ibis Theristicus caerulescens GCA_020745775.1_bTheCae1.pri.cur SAMN22550094 PRJNA774297 2021-11-05
82 red-crested turaco Tauraco erythrolophus GCF_000709365.1_ASM70936v1 SAMN02339893 PRJNA212908 2014-06-25
83 red-fronted tinkerbird Pogoniulus pusillus GCA_015220805.1_bPogPus1.pri SAMN15098508 PRJNA637953 2020-11-03
84 red-legged partridge Alectoris rufa GCA_019345075.1_ASM1934507v1 SAMN16083939 PRJNA662415 2021-07-26
85 red-legged seriema Cariama cristata GCF_000690535.1_ASM69053v1 SAMN02318733 PRJNA212889 2014-05-12
86 red-throated loon Gavia stellata GCF_000690875.1_ASM69087v1 SAMN02324832 PRJNA212895 2014-05-13
87 rhinoceros hornbill Buceros rhinoceros silvestris GCF_000710305.1_ASM71030v1 SAMN02318191 PRJNA212887 2014-06-25
88 rifleman (VGP 2021) Acanthisitta chloris GCA_016904835.1_bAcaChl1.pri SAMN16442762 PRJNA561954 2021-02-17
89 ring-necked pheasant Phasianus colchicus GCF_004143745.1_ASM414374v1 SAMN08888240 PRJNA449162 2019-02-06
90 rock pigeon Columba livia GCF_000337935.1_Cliv_1.0 SAMN02981415 PRJNA167554 2013-02-11
91 ruddy duck Oxyura jamaicensis GCF_011077185.1_BPBGC_Ojam_1.0 SAMN13257492 PRJNA588796 2020-03-10
92 ruff Calidris pugnax GCF_001431845.1_ASM143184v1 SAMN03491621 PRJNA281024 2015-11-04
93 rufous-necked snowfinch Pyrgilauda ruficollis GCF_017590135.1_ASM1759013v1 SAMN18252884 PRJNA417520 2021-03-26
94 saffron-crested tyrant-manakin Neopelma chrysocephalum GCF_003984885.1_ASM398488v2 SAMN08784363 PRJNA445439 2018-12-28
95 Saker falcon Falco cherrug GCF_000337975.1_F_cherrug_v1.0 SAMN02981426 PRJNA168071 2013-02-05
96 small tree finch (2019) Camarhynchus parvulus GCF_901933205.1_STF_HiC SAMEA5603054 PRJEB32528 2019-09-06
97 small tree finch (2020) Camarhynchus parvulus GCA_902806625.1_Camarhynchus_parvulus_V1.1 SAMEA6542012 PRJEB36748 2020-03-21
98 South Island takahe (VGP alternate 2021) Porphyrio hochstetteri GCA_020801775.1_bPorHoc1.pat.decon SAMN22550412 PRJNA774332 2021-11-08
99 South Island takahe (VGP primary 2021) Porphyrio hochstetteri GCA_020800305.1_bPorHoc1.mat.Z.cur SAMN22550412 PRJNA774331 2021-11-08
100 speckled mousebird Colius striatus GCF_000690715.1_ASM69071v1 SAMN02324230 PRJNA212892 2014-05-13
101 sunbittern Eurypyga helias GCF_000690775.1_ASM69077v1 SAMN02324546 PRJNA212893 2014-05-13
102 Suruca trogon Trogon surrucura GCA_020746105.1_bTroSur1.pri.cur SAMN22550082 PRJNA774295 2021-11-05
103 Swainson's thrush Catharus ustulatus GCF_009819885.2_bCatUst1.pri.v2 SAMN12618602 PRJNA561933 2020-12-22
104 swan goose (Sichuan white goose 2017) Anser cygnoides GCF_002166845.1_GooseV1.0 SAMN02898389 PRJNA253976 2017-06-02
105 swan goose (Tianfu 2020) Anser cygnoides GCA_013030995.1_ASM1303099v1 SAMN13281505 PRJNA589208 2020-05-11
106 swan goose (Zhedong 2015) Anser cygnoides domesticus GCF_000971095.1_AnsCyg_PRJNA183603_v1.0 SAMN01830643 PRJNA183603 2015-04-08
107 Tibetan ground-tit Pseudopodoces humilis GCF_000331425.1_PseHum1.0 SAMN02981490 PRJNA175930 2013-01-11
108 turkey Meleagris gallopavo GCF_000146605.3_Turkey_5.1 SAMN02981253 PRJNA42129 2014-11-24
109 turkey (WU_HG_1 2021) Meleagris gallopavo GCA_905368555.1_MGAL_WU_HG_1.0 SAMEA7852930 PRJEB42643 2021-03-26
110 whiskered treeswift Hemiprocne comata GCA_020745705.1_bHemCom1.pri.cur SAMN22588383 PRJNA774831 2021-11-05
111 white leghorn layer paternal (VGP 2021) Gallus gallus GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w SAMN15960293 PRJNA660758 2021-10-01
112 white wagtail Motacilla alba alba GCF_015832195.1_Motacilla_alba_V1.0_pri SAMN16093224 PRJNA662706 2020-12-08
113 white-ruffed manakin Corapipo altera GCF_003945725.1_ASM394572v1 SAMN10424454 PRJNA505529 2018-12-14
114 white-rumped snowfinch Onychostruthus taczanowskii GCF_017590055.1_ASM1759005v1 SAMN18252883 PRJNA417520 2021-03-26
115 white-tailed eagle Haliaeetus albicilla GCF_000691405.1_ASM69140v1 SAMN02333670 PRJNA212896 2014-05-15
116 white-tailed ptarmigan Lagopus leucura GCF_019238085.1_USGS_WTPT01 SAMN12859112 PRJNA574481 2021-07-15
117 white-tailed tropicbird Phaethon lepturus GCF_000687285.1_ASM68728v1 SAMN02339888 PRJNA212902 2014-05-08
118 white-throated sparrow Zonotrichia albicollis GCF_000385455.1_Zonotrichia_albicollis-1.0.1 SAMN02981528 PRJNA197293 2013-04-30
119 white-throated tinamou Tinamus guttatus GCF_000705375.1_ASM70537v2 SAMN02316659 PRJNA212876 2014-08-05
120 willow flycatcher Empidonax traillii GCF_003031625.1_ASM303162v1 SAMN08663748 PRJNA437496 2018-04-03
121 wire-tailed manakin (2020) Pipra filicauda GCF_003945595.2_ASM394559v2 SAMN08774045 PRJNA445296 2020-12-01
122 yellow-throated sandgrouse Pterocles gutturalis GCF_000699245.1_ASM69924v1 SAMN02339892 PRJNA212906 2014-06-09
123 zebra finch (v1.4 2021) Taeniopygia guttata GCF_003957565.2_bTaeGut1.4.pri SAMN02981239 PRJNA489098 2021-05-04

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 154 assemblies assembly stats track stats
Fungi 416 assemblies assembly stats track stats
VGP - Vertebrate Genome Project 233 assemblies assembly stats track stats
legacy/superseded 139 assemblies assembly stats track stats