Legacy Genomes assembly hubs

Assemblies from NCBI/Genbank/Refseq sources, subset of legacy 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/legacy/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 Legacy 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.


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 aardvark (BS58 2019 Broad) Orycteropus afer GCA_004365145.1_OryAfe_v1_BIUU SAMN07678101 PRJNA399461 2019-03-22
2 African clawed frog (2016) Xenopus laevis GCF_001663975.1_Xenopus_laevis_v2 SAMN04518361 PRJNA313213 2016-08-09
3 African savanna elephant (2009 genbank) Loxodonta africana GCA_000001905.1_Loxafr3.0 SAMN02953622 PRJNA12569 2009-07-15
4 alpaca (2015 BGI) Vicugna pacos huacaya GCA_000767525.1_Vi_pacos_V1.0 SAMN02996813 PRJNA233565 2015-02-11
5 American beaver (US014 2019 Broad) Castor canadensis GCA_004027675.1_CasCan_v1_BIUU SAMN07678136 PRJNA399431 2019-01-16
6 American bison (2014 genbank) Bison bison bison GCA_000754665.1_Bison_UMD1.0 SAMN02947321 PRJNA257088 2014-10-08
7 American pika 3.0 (2012 Broad genbank) Ochotona princeps GCA_000292845.1_OchPri3.0 SAMN00767999 PRJNA74593 2012-08-27
8 Amur tiger (TaeGuk 2013 genbank) Panthera tigris altaica GCA_000464555.1_PanTig1.0 SAMN02086964 PRJNA182708 2013-09-06
9 Arabian camel (2014 genbank) Camelus dromedarius GCA_000767585.1_PRJNA234474_Ca_dromedarius_V1.0 SAMN03000646 PRJNA234474 2014-10-21
10 Arctic fox (US066 2019 Broad) Vulpes lagopus GCA_004023825.1_VulLag_v1_BIUU SAMN07678118 PRJNA399424 2019-01-15
11 ass (Maral har 2015 genbank) Equus asinus GCA_001305755.1_ASM130575v1 SAMN03010633 PRJNA259598 2015-10-02
12 Atlantic herring (v1) Clupea harengus GCF_900700415.1_Ch_v2.0.2 SAMEA5339254 PRJEB31270 2019-04-16
13 B.malayi (v3 2008 agent of lymphatic filariasis) Brugia malayi GCF_000002995.3_ASM299v2 SAMN02953652 PRJNA10729 2008-03-04
14 Bactrian camel (Alxa 2014 genbank) Camelus bactrianus GCA_000767855.1_Ca_bactrianus_MBC_1.0 SAMN02953968 PRJNA183605 2014-10-23
15 barn owl BGI_N341 (2014) Tyto alba GCF_000687205.1_ASM68720v1 SAMN02339894 PRJNA212909 2014-05-08
16 barn owl (2020) Tyto alba alba GCF_902150015.1_genome_assembly_l500 SAMEA5733888 PRJEB33158 2020-02-10
17 black-legged tick (U.Maryland v1 2021) Ixodes scapularis GCF_016920785.1_Ixodes_scapularus_ComboLowHiFi SAMN16793453 PRJNA678334 2021-02-23
18 black snub-nosed monkey genbank Rhinopithecus bieti GCA_001698545.1_ASM169854v1 SAMN02786331 PRJNA315476 2016-08-03
19 Bolivian squirrel monkey (2011) Saimiri boliviensis boliviensis GCF_000235385.1_SaiBol1.0 SAMN02981369 PRJNA67945 2011-11-17
20 brown bear (v1 2018) Ursus arctos horribilis GCF_003584765.1_ASM358476v1 SAMN09907428 PRJNA487641 2018-09-20
21 California sea lion (BS06 2019 Broad) Zalophus californianus GCA_004024565.1_ZalCal_v1_BIUU SAMN07678053 PRJNA399369 2019-01-15
22 Cape golden mole (BS56 2019 Broad) Chrysochloris asiatica GCA_004027935.1_ChrAsi_v1_BIUU SAMN07678135 PRJNA399474 2019-01-16
23 cassava (v6 AM560-2 2016 DOE) Manihot esculenta GCF_001659605.1_Manihot_esculenta_v6 SAMN04116956 PRJNA234389 2016-06-10
24 cattle (Hereford 2015) Bos taurus GCA_000003205.6_Btau_5.0.1 SAMN02898106 PRJNA12555 2015-11-19
25 cheetah (AJU 981 2015) Acinonyx jubatus GCA_001443585.1_aciJub1 SAMN04127588 PRJNA297632 2015-11-13
26 chimpanzee genbank Pan troglodytes GCA_002880755.3_Clint_PTRv2 SAMN06272697 PRJNA369439 2018-01-19
27 China rose (Old Blush v1 2018) Rosa chinensis GCF_002994745.1_RchiOBHm-V2 SAMN07737764 PRJNA413292 2018-03-13
28 Chinese hamster (17A/GY CHO 2018) Cricetulus griseus GCF_003668045.1_CriGri-PICR SAMN07140313 PRJNA389969 2018-10-21
29 Chinese pangolin (MPE899 2014 WashU) Manis pentadactyla GCA_000738955.1_M_pentadactyla-1.1.1 SAMN01943338 PRJNA20331 2014-08-11
30 common bottlenose dolphin (MMES2002162SC 2016 genbank) Tursiops truncatus GCA_001922835.1_NIST_Tur_tru_v1 SAMN06114300 PRJNA356464 2016-12-28
31 common carp (2014) Cyprinus carpio GCF_000951615.1_common_carp_genome SAMEA2757102 PRJEB7241 2014-11-03
32 common cuckoo (BGI 2014) Cuculus canorus GCF_000709325.1_ASM70932v1 SAMN02298149 PRJNA212870 2014-06-17
33 common house spider (v2 2017) Parasteatoda tepidariorum GCF_000365465.2_Ptep_2.0 SAMN02364452 PRJNA167405 2017-04-14
34 common vampire bat (DRU21DN04 2018 genbank) Desmodus rotundus GCA_002940915.2_ASM294091v2 SAMN07783852 PRJNA414273 2018-02-23
35 Coquerel's sifaka 6110/Marcella (2015 genbank) Propithecus coquereli GCA_000956105.1_Pcoq_1.0 SAMN03121823 PRJNA251429 2015-03-23
36 crab-eating macaque WashU 2013 genbank Macaca fascicularis GCA_000364345.1_Macaca_fascicularis_5.0 SAMN00811240 PRJNA20409 2013-06-12
37 crab-eating macaque WashU 2013 refseq Macaca fascicularis GCF_000364345.1_Macaca_fascicularis_5.0 SAMN00811240 PRJNA20409 2013-06-12
38 degu (3935 2012 genbank) Octodon degus GCA_000260255.1_OctDeg1.0 SAMN00769067 PRJNA74595 2012-05-01
39 dog (BS72 2019 Broad) Canis lupus familiaris GCA_004027395.1_CanFam_VD_v1_BIUU SAMN07678141 PRJNA399441 2019-01-16
40 domestic ferret (Sable ID 1420 FGSC 2011) Mustela putorius furo GCF_000215625.1_MusPutFur1.0 SAMN00149631 PRJNA59869 2011-06-02
41 domestic guinea pig (2N 2008 genbank) Cavia porcellus GCA_000151735.1_Cavpor3.0 SAMN02981223 PRJNA12583 2008-03-03
42 downy woodpecker (BGI 2014) Picoides pubescens GCF_000699005.1_ASM69900v1 SAMN02314405 PRJNA212874 2014-06-06
43 Egyptian rousette (US006 2019 Broad) Rousettus aegyptiacus GCA_004024865.1_RouAeg_v1_BIUU SAMN07678121 PRJNA399428 2019-01-15
44 elephant shark (2013) Callorhinchus milii GCF_000165045.1_Callorhinchus_milii-6.1.3 SAMN00000800 PRJNA18361 2013-12-11
45 Eurasian water vole (v1 2020) Arvicola amphibius GCF_903992535.1_mArvAmp1.1 SAMEA994740 PRJEB39550 2020-08-06
46 Florida manatee (Lorelei 2012 genbank) Trichechus manatus latirostris GCA_000243295.1_TriManLat1.0 SAMN00632092 PRJNA68243 2012-01-23
47 fly D.yakuba (2018) Drosophila yakuba GCF_000005975.2_dyak_caf1 SAMN02952910 PRJNA12366 2006-06-27
48 fly D.yakuba (v1 2021) Drosophila yakuba GCF_016746365.1_Prin_Dyak_Tai18E2_2.0 SAMN15573791 PRJNA647028 2021-01-25
49 giant panda Ailuropoda melanoleuca GCF_000004335.2_AilMel_1.0 SAMN00008160 PRJNA38683 2009-12-15
50 goat (San Clemente 2016 USDA genbank) Capra hircus GCA_001704415.1_ARS1 SAMN03863711 PRJNA290100 2016-08-24
51 golden hamster (Baylor 2013 genbank) Mesocricetus auratus GCA_000349665.1_MesAur1.0 SAMN00769068 PRJNA77669 2013-03-29
52 golden snub-nosed monkey (2014 Novogene) Rhinopithecus roxellana GCA_000769185.1_Rrox_v1 SAMN02427086 PRJNA230020 2014-10-28
53 gray mouse lemur genbank Microcebus murinus GCA_000165445.3_Mmur_3.0 SAMN06275470 PRJNA19967 2017-02-06
54 great roundleaf bat (ML-2016 2016 genbank) Hipposideros armiger GCA_001890085.1_ASM189008v1 SAMN03177460 PRJNA267039 2016-12-06
55 greater mouse-eared bat (2019 Broad) Myotis myotis GCA_004026985.1_MyoMyo_v1_BIUU SAMN07678038 PRJNA399444 2019-01-16
56 green algae C.reinhardtii CC-503 cw92 (v1 2007) Chlamydomonas reinhardtii GCF_000002595.1_v3.0 SAMN02953692 PRJNA12260 2007-10-15
57 green monkey 1994-021 (2014 genbank) Chlorocebus sabaeus GCA_000409795.2_Chlorocebus_sabeus_1.1 SAMN01760484 PRJNA168621 2014-03-25
58 green sea turtle (BGI 2013) Chelonia mydas GCF_000344595.1_CheMyd_1.0 SAMN02981410 PRJNA104937 2013-03-18
59 green sea turtle (v1 2020) Chelonia mydas GCF_015237465.1_rCheMyd1.pri SAMN12612360 PRJNA561941 2020-11-05
60 Hawaiian monk seal (2017 Johns Hopkins U) Neomonachus schauinslandi GCF_002201575.1_ASM220157v1 SAMN06841387 PRJNA384558 2017-06-20
61 hooded crow (2017) Corvus cornix cornix GCF_000738735.2_ASM73873v2 SAMN02143031 PRJNA192205 2017-03-08
62 horse (Twilight 2007 genbank) Equus caballus GCA_000002305.1_EquCab2.0 SAMN02953672 PRJNA18661 2007-10-29
63 house mouse Mus musculus GCF_000001635.26_GRCm38.p6 n/a PRJNA20689 2017-09-15
64 Indian medaka Oryzias melastigma GCF_002922805.1_Om_v0.7.RACA SAMN07596545 PRJNA401159 2018-02-07
65 Jamaican fruit-eating bat (US092 2019 Broad) Artibeus jamaicensis GCA_004027435.1_ArtJam_v1_BIUU SAMN07678132 PRJNA399471 2019-01-16
66 Japanese quail Coturnix japonica GCF_001577835.1_Coturnix_japonica_2.0 SAMN03989050 PRJNA292031 2016-03-01
67 leatherback sea turtle (v3 2020) Dermochelys coriacea GCF_009764565.2_rDerCor1.pri.v3 SAMN12629498 PRJNA561993 2020-12-09
68 lesser Egyptian jerboa (JJ0015 2012 genbank) Jaculus jaculus GCA_000280705.1_JacJac1.0 SAMN00728442 PRJNA72445 2012-07-30
69 lettuce (Salinas v1 2018) Lactuca sativa GCF_002870075.1_Lsat_Salinas_v7 SAMN01730979 PRJNA173551 2018-01-09
70 leopard (Maewha 2016 genbank) Panthera pardus GCA_001857705.1_PanPar1.0 SAMN04347630 PRJNA306701 2016-11-16
71 Ma's night monkey genbank Aotus nancymaae GCA_000952055.2_Anan_2.0 SAMN03121886 PRJNA251539 2017-06-09
72 Malayan pangolin (MP_PG03-UM 2016 genbank) Manis javanica GCA_001685135.1_ManJav1.0 SAMN02935387 PRJNA256023 2016-07-14
73 malo sina (v1 2012) Oryza brachyantha GCF_000231095.1_Oryza_brachyantha.v1.4b SAMN02981362 PRJNA70533 2012-01-19
74 mangrove rivulus Kryptolebias marmoratus GCF_001649575.1_ASM164957v1 SAMN04622665 PRJNA317650 2016-05-22
75 meerkat (BS45 2019 Broad) Suricata suricatta GCA_004023905.1_SurSur_v1_BIUU SAMN07678040 PRJNA399357 2019-01-15
76 minke whale (2013 genbank) Balaenoptera acutorostrata scammoni GCA_000493695.1_BalAcu1.0 SAMN02192642 PRJNA72723 2013-10-31
77 Mongolian gerbil (US013 2019 Broad) Meriones unguiculatus GCA_004026785.1_MerUng_v1_BIUU SAMN07678137 PRJNA399432 2019-01-16
78 naked mole-rat (NMR 29 2012 genbank) Heterocephalus glaber GCA_000247695.1_HetGla_female_1.0 SAMN00714537 PRJNA72441 2012-02-17
79 narwhal (BS41 2019 Broad) Monodon monoceros GCA_004026685.1_MonMon_M_v1_BIUU SAMN07678024 PRJNA399349 2019-01-16
80 New South Wales waratah (AGSP 2013) Amborella trichopoda GCF_000471905.2_AMTR1.0 SAMN02313977 PRJNA212863 2013-09-30
81 nine-banded armadillo (3-136 2012 Baylor genbank) Dasypus novemcinctus GCA_000208655.2_Dasnov3.0 SAMN02953623 PRJNA12594 2012-01-06
82 northern white-cheeked gibbon (2012 GGSC) Nomascus leucogenys GCA_000146795.3_Nleu_3.0 SAMN02981257 PRJNA13975 2012-12-08
83 Norway rat BN7 genbank Rattus norvegicus GCA_015227675.2_mRatBN7.2 SAMN16261960 PRJNA662791 2020-11-10
84 olive baboon (2017 HGSC RefSeq) Papio anubis GCF_000264685.3_Panu_3.0 SAMN02981400 PRJNA54005 2017-04-20
85 olive baboon (2017 HGSC genbank) Papio anubis GCA_000264685.2_Panu_3.0 SAMN02981400 PRJNA54005 2017-04-20
86 pike-perch Sander lucioperca GCF_008315115.1_SLUC_FBN_1 SAMN12618724 PRJNA561467 2019-09-06
87 platypus (v1 2019) Ornithorhynchus anatinus GCF_004115215.1_mOrnAna1.p.v1 SAMN08537700 PRJNA489114 2019-02-07
88 polar bear (Baiyulong BGI 2014 genbank) Ursus maritimus GCA_000687225.1_UrsMar_1.0 SAMN02729226 PRJNA210951 2014-05-09
89 Przewalski's horse (Burgud 2014 genbank) Equus przewalskii GCA_000696695.1_Burgud SAMN02808398 PRJNA200657 2014-06-05
90 puma (SC36_Marlon 2018 genbank) Puma concolor GCA_003327715.1_PumCon1.0 SAMN08662999 PRJNA437459 2018-07-19
91 pygmy chimpanzee (Ulindi genbank 2015) Pan paniscus GCA_000258655.2_panpan1.1 SAMEA1029457 PRJNA49285 2015-08-18
92 rabbit (Thorbecke 2009 Broad genbank) Oryctolagus cuniculus GCA_000003625.1_OryCun2.0 SAMN02953624 PRJNA12819 2009-10-20
93 Rhesus monkey (2015 Baylor) Macaca mulatta GCA_000772875.3_Mmul_8.0.1 n/a PRJNA214746 2015-11-30
94 rifleman (BGI 2014) Acanthisitta chloris GCF_000695815.1_ASM69581v1 SAMN02318032 PRJNA212877 2014-05-27
95 ring-tailed lemur BS26 Broad 2019 Lemur catta GCA_004024665.1_LemCat_v1_BIUU SAMN07678092 PRJNA399402 2019-01-15
96 Rio pearlfish (Nwh7 v1 2020) Nematolebias whitei GCF_014905685.1_NemWhi1 SAMN12588121 PRJNA560526 2020-10-22
97 Ryukyu mouse (2017 EBI genbank) Mus caroli GCA_900094665.2_CAROLI_EIJ_v1.1 SAMEA3367631 PRJEB14895 2017-04-28
98 sea otter (GAN:26980312 2017 genbank) Enhydra lutris kenyoni GCA_002288905.2_ASM228890v2 SAMN07211055 PRJNA388419 2017-09-11
99 Siamese fighting fish (v2 2019) Betta splendens GCF_900634795.2_fBetSpl5.2 SAMEA104381735 PRJEB30365 2019-03-20
100 silvery gibbon Hylobates moloch GCF_009828535.1_HMol SAMN12851060 PRJNA575281 2020-01-03
101 southern white rhinoceros (SDZICR_KB13650 2012 genbank) Ceratotherium simum simum GCA_000283155.1_CerSimSim1.0 SAMN00778988 PRJNA74583 2012-07-31
102 soybean (US DOE JGI-PGF v1 2018) Glycine max GCF_000004515.5_Glycine_max_v2.1 SAMN00002965 PRJNA19861 2018-07-24
103 Sumatran orangutan (2018 genbank) Pongo abelii GCA_002880775.3_Susie_PABv2 SAMN06275555 PRJNA369439 2018-01-19
104 Tasmanian devil Sarcophilus harrisii GCF_000189315.1_Devil_ref_v7.0 SAMN02953780 PRJNA51853 2011-02-17
105 thirteen-lined ground squirrel (2011) Ictidomys tridecemlineatus GCF_000236235.1_SpeTri2.0 SAMN00210855 PRJNA61725 2011-11-29
106 Ugandan red Colobus Piliocolobus tephrosceles GCF_002776525.2_ASM277652v2 SAMN07735529 PRJNA413051 2018-09-11
107 Upper Galilee mountains blind mole rat (#2095 2014 genbank) Nannospalax galili GCA_000622305.1_S.galili_v1.0 SAMN02299330 PRJNA213569 2014-06-05
108 valley oak (v3.0 2019) Quercus lobata GCF_001633185.1_ValleyOak3.0 SAMN10584531 PRJNA308314 2019-01-11
109 water buffalo (Mediterranean 2013) Bubalus bubalis GCA_000471725.1_UMD_CASPUR_WB_2.0 SAMN02191888 PRJNA207334 2013-09-30
110 Weddell seal (WS11-02 2013 genbank) Leptonychotes weddellii GCA_000349705.1_LepWed1.0 SAMN00672463 PRJNA68235 2013-03-29
111 western European hedgehog (2012 genbank) Erinaceus europaeus GCA_000296755.1_EriEur2.0 SAMN00760989 PRJNA74585 2012-09-19
112 western lowland gorilla (Susie 2016) Gorilla gorilla gorilla GCA_900006655.3_Susie3 SAMEA3541598 PRJEB10880 2016-12-22
113 western painted turtle (v303 2014) Chrysemys picta bellii GCF_000241765.3_Chrysemys_picta_bellii-3.0.3 SAMN02713681 PRJNA78657 2014-03-31
114 white-footed mouse Peromyscus leucopus GCF_004664715.1_Pero_0.1 SAMN03488028 PRJNA281425 2019-04-05
115 white-tailed deer (Pink-7 2017 genbank) Odocoileus virginianus texanus GCA_002102435.1_Ovir.te_1.0 SAMN05363940 PRJNA317745 2017-04-20
116 white-tufted-ear marmoset (CJ-08-46 2017) Callithrix jacchus GCA_002754865.1_ASM275486v1 SAMN07586072 PRJNA401030 2017-11-06
117 white-tufted-ear marmoset (2010 Wash U) Callithrix jacchus GCF_000004665.1_Callithrix_jacchus-3.2 SAMN02981242 PRJNA20401 2010-01-22
118 white-tufted-ear marmoset (cj1700 genbank) Callithrix jacchus GCA_009663435.1_Callithrix_jacchus_cj1700_1.0 SAMN12783337 PRJNA566173 2019-11-15
119 wire-tailed manakin (2018) Pipra filicauda GCF_003945595.1_ASM394559v1 SAMN08774045 PRJNA445296 2018-12-14
120 woodchuck Marmota monax GCA_901343595.1_MONAX5 SAMEA91498168 PRJEB19462 2019-09-13
121 Yangtze finless porpoise (v1 2018) Neophocaena asiaeorientalis asiaeorientalis GCF_003031525.1_Neophocaena_asiaeorientalis_V1 SAMN05831577 PRJNA343136 2018-04-03
122 Yangtze River dolphin (BGI 2013 genbank) Lipotes vexillifer GCA_000442215.1_Lipotes_vexillifer_v1 SAMN02953859 PRJNA174066 2013-07-31
123 yellow-bellied marmot Marmota flaviventris GCF_003676075.1_ASM367607v1 SAMN10078668 PRJNA491472 2018-10-22
124 zebra finch (v1 2019) Taeniopygia guttata GCF_003957565.1_bTaeGut1_v1.p SAMN02981239 PRJNA489098 2019-05-16
125 zebu cattle (Nelore 2014 genbank) Bos indicus GCA_000247795.2_Bos_indicus_1.0 SAMN02953802 PRJNA72827 2014-11-25

Additional hubs with collections of assemblies
Collection Hub index pages: Assembly statistics: Track statistics:
Primates 49 assemblies assembly stats track stats
Mammals 276 assemblies assembly stats track stats
Birds 112 assemblies assembly stats track stats
Fishes 128 assemblies assembly stats track stats
other vertebrates 46 assemblies assembly stats track stats
Invertebrates 396 assemblies assembly stats track stats
Plants 146 assemblies assembly stats track stats
Fungi 415 assemblies assembly stats track stats
VGP - Vertebrate Genome Project 233 assemblies assembly stats track stats
legacy/superseded 125 assemblies assembly stats track stats