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 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 African clawed frog (2016) Xenopus laevis GCF_001663975.1_Xenopus_laevis_v2 SAMN04518361 PRJNA313213 2016-08-09
2 black-legged tick (U.Maryland v1 2021) Ixodes scapularis GCF_016920785.1_Ixodes_scapularus_ComboLowHiFi SAMN16793453 PRJNA678334 2021-02-23
3 Bolivian squirrel monkey (2011) Saimiri boliviensis boliviensis GCF_000235385.1_SaiBol1.0 SAMN02981369 PRJNA67945 2011-11-17
4 China rose (Old Blush v1 2018) Rosa chinensis GCF_002994745.1_RchiOBHm-V2 SAMN07737764 PRJNA413292 2018-03-13
5 Chinese hamster Cricetulus griseus GCF_003668045.1_CriGri-PICR SAMN07140313 PRJNA389969 2018-10-21
6 elephant shark (2013) Callorhinchus milii GCF_000165045.1_Callorhinchus_milii-6.1.3 SAMN00000800 PRJNA18361 2013-12-11
7 Eurasian water vole (v1 2020) Arvicola amphibius GCF_903992535.1_mArvAmp1.1 SAMEA994740 PRJEB39550 2020-08-06
8 fly D.yakuba (2018) Drosophila yakuba GCF_000005975.2_dyak_caf1 SAMN02952910 PRJNA12366 2006-06-27
9 giant panda Ailuropoda melanoleuca GCF_000004335.2_AilMel_1.0 SAMN00008160 PRJNA38683 2009-12-15
10 hooded crow (2017) Corvus cornix cornix GCF_000738735.2_ASM73873v2 SAMN02143031 PRJNA192205 2017-03-08
11 house mouse Mus musculus GCF_000001635.26_GRCm38.p6 n/a PRJNA20689 2017-09-15
12 Indian medaka Oryzias melastigma GCF_002922805.1_Om_v0.7.RACA SAMN07596545 PRJNA401159 2018-02-07
13 Japanese quail Coturnix japonica GCF_001577835.1_Coturnix_japonica_2.0 SAMN03989050 PRJNA292031 2016-03-01
14 malo sina (v1 2012) Oryza brachyantha GCF_000231095.1_Oryza_brachyantha.v1.4b SAMN02981362 PRJNA70533 2012-01-19
15 mangrove rivulus Kryptolebias marmoratus GCF_001649575.1_ASM164957v1 SAMN04622665 PRJNA317650 2016-05-22
16 Norway rat BN7 genbank Rattus norvegicus GCA_015227675.2_mRatBN7.2 SAMN16261960 PRJNA662791 2020-11-10
17 olive baboon Papio anubis GCF_000264685.3_Panu_3.0 SAMN02981400 PRJNA54005 2017-04-20
18 pike-perch Sander lucioperca GCF_008315115.1_SLUC_FBN_1 SAMN12618724 PRJNA561467 2019-09-06
19 platypus (2019 v1) Ornithorhynchus anatinus GCF_004115215.1_mOrnAna1.p.v1 SAMN08537700 PRJNA489114 2019-02-07
20 Siamese fighting fish (v2 2019) Betta splendens GCF_900634795.2_fBetSpl5.2 SAMEA104381735 PRJEB30365 2019-03-20
21 silvery gibbon Hylobates moloch GCF_009828535.1_HMol SAMN12851060 PRJNA575281 2020-01-03
22 soybean (US DOE JGI-PGF v1 2018) Glycine max GCF_000004515.5_Glycine_max_v2.1 SAMN00002965 PRJNA19861 2018-07-24
23 Tasmanian devil Sarcophilus harrisii GCF_000189315.1_Devil_ref_v7.0 SAMN02953780 PRJNA51853 2011-02-17
24 thirteen-lined ground squirrel (2011) Ictidomys tridecemlineatus GCF_000236235.1_SpeTri2.0 SAMN00210855 PRJNA61725 2011-11-29
25 Ugandan red Colobus Piliocolobus tephrosceles GCF_002776525.2_ASM277652v2 SAMN07735529 PRJNA413051 2018-09-11
26 white-footed mouse Peromyscus leucopus GCF_004664715.1_Pero_0.1 SAMN03488028 PRJNA281425 2019-04-05
27 white-tufted-ear marmoset Callithrix jacchus GCF_000004665.1_Callithrix_jacchus-3.2 SAMN02981242 PRJNA20401 2010-01-22
28 white-tufted-ear marmoset Callithrix jacchus GCA_009663435.1_Callithrix_jacchus_cj1700_1.0 SAMN12783337 PRJNA566173 2019-11-15
29 wire-tailed manakin (2018) Pipra filicauda GCF_003945595.1_ASM394559v1 SAMN08774045 PRJNA445296 2018-12-14
30 woodchuck Marmota monax GCA_901343595.1_MONAX5 SAMEA91498168 PRJEB19462 2019-09-13
31 Yangtze finless porpoise (v1) Neophocaena asiaeorientalis asiaeorientalis GCF_003031525.1_Neophocaena_asiaeorientalis_V1 SAMN05831577 PRJNA343136 2018-04-03
32 yellow-bellied marmot Marmota flaviventris GCF_003676075.1_ASM367607v1 SAMN10078668 PRJNA491472 2018-10-22
33 zebra finch (v1 2019) Taeniopygia guttata GCF_003957565.1_bTaeGut1_v1.p SAMN02981239 PRJNA489098 2019-05-16

Additional hubs with collections of assemblies
Collection Hub index pages: Assembly statistics: Track statistics:
Primates 31 assemblies assembly stats track stats
Mammals 157 assemblies assembly stats track stats
Birds 86 assemblies assembly stats track stats
Fishes 121 assemblies assembly stats track stats
other vertebrates 45 assemblies assembly stats track stats
Invertebrates 249 assemblies assembly stats track stats
Plants 138 assemblies assembly stats track stats
Fungi 390 assemblies assembly stats track stats
VGP - Vertebrate Genome Project 210 assemblies assembly stats track stats
legacy/superseded 33 assemblies assembly stats track stats