How do I get a list of all species with a fasta genome in UCSC?
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7.0 years ago
endrebak ▴ 970

I want to get a list of all genomes in UCSC like mm10, hg38 etc. Is there a simple way to do that?

UCSC • 1.9k views
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GenoMax 144k

CurrentGenomes at UCSC are available in this directory.

 $ curl -l ftp://hgdownload.soe.ucsc.edu/goldenPath/currentGenomes/
    .
    ..
    Ailuropoda_melanoleuca
    Anolis_carolinensis
    Anopheles_gambiae
    Apis_mellifera
    Aplysia_californica
    Bos_taurus
    Branchiostoma_floridae
    Caenorhabditis_brenneri
    Caenorhabditis_briggsae
    Caenorhabditis_elegans
    Caenorhabditis_japonica
    Caenorhabditis_remanei
    Callithrix_jacchus
    Canis_familiaris
    Cavia_porcellus
    Ceratotherium_simum
    Choloepus_hoffmanni
    Chrysemys_picta_bellii
    Ciona_intestinalis
    Dasypus_novemcinctus
    Dipodomys_ordii
    Drosophila_ananassae
    Drosophila_erecta
    Drosophila_grimshawi
    Drosophila_melanogaster
    Drosophila_mojavensis
    Drosophila_persimilis
    Drosophila_pseudoobscura
    Drosophila_sechellia
    Drosophila_simulans
    Drosophila_virilis
    Drosophila_yakuba
    Sorex_araneus
    Equus_caballus
    Rattus_norvegicus
    Fugu_rubripes
    Gadus_morhua
    Geospiza_fortis
    Heterocephalus_glaber
    Homo_sapiens
    Latimeria_chalumnae
    Loxodonta_africana
    Macropus_eugenii
    Meleagris_gallopavo
    Melopsittacus_undulatus
    Microcebus_murinus
    Monodelphis_domestica
    Mus_musculus
    Mustela_putorius_furo
    Myotis_lucifugus
    Nomascus_leucogenys
    Ebola_virus
    Oreochromis_niloticus
    Ornithorhynchus_anatinus
    Oryctolagus_cuniculus
    Oryzias_latipes
    Otolemur_garnettii
    Papio_anubis
    Papio_hamadryas
    Petromyzon_marinus
    Pongo_abelii
    Pongo_pygmaeus_abelii
    Pristionchus_pacificus
    Procavia_capensis
    Pteropus_vampyrus
    Danio_rerio
    SARS_coronavirus
    Saccharomyces_cerevisiae
    Saimiri_boliviensis
    Sarcophilus_harrisii
    Spermophilus_tridecemlineatus
    Strongylocentrotus_purpuratus
    Sus_scrofa
    Tarsius_syrichta
    Takifugu_rubripes
    Felis_catus
    Tetraodon_nigroviridis
    Trichechus_manatus_latirostris
    Tupaia_belangeri
    Tursiops_truncatus
    Xenopus_tropicalis
    Echinops_telfairi
    Ovis_aries
    Vicugna_pacos
    Alligator_mississippiensis
    Balaenoptera_acutorostrata_scammoni
    Cricetulus_griseus
    Erinaceus_europaeus
    Taeniopygia_guttata
    Callorhinchus_milii
    Ochotona_princeps
    Apteryx_australis
    Macaca_fascicularis
    Rhesus_macaque
    Gallus_gallus
    Pan_troglodytes
    Gorilla_gorilla_gorilla
    Chlorocebus_sabaeus
    Nasalis_larvatus
    Nanorana_parkeri
    Manis_pentadactyla
    Aquila_chrysaetos_canadensis
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Thanks, I actually wanted the abbrevs like hg38 and so on but this is good too.

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7.0 years ago
$ mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D  hgcentral   -e 'select * from  dbDb \G'
*************************** 1. row ***************************
          name: hg38
   description: Dec. 2013 (GRCh38/hg38)
       nibPath: /gbdb/hg38
      organism: Human
    defaultPos: chr1:11102837-11267747
        active: 1
      orderKey: 50
        genome: Human
scientificName: Homo sapiens
      htmlPath: /gbdb/hg38/html/description.html
      hgNearOk: 1
        hgPbOk: 0
    sourceName: GRCh38 Genome Reference Consortium Human Reference 38 (GCA_000001405.2)
         taxId: 9606
*************************** 2. row ***************************
          name: balAcu1
   description: Oct. 2013 (BalAcu1.0/balAcu1)
       nibPath: /gbdb/balAcu1
      organism: Minke whale
    defaultPos: KI537194:1947619-1969416
        active: 1
      orderKey: 13475
        genome: Minke whale
scientificName: Balaenoptera acutorostrata scammoni
      htmlPath: /gbdb/balAcu1/html/description.html
      hgNearOk: 0
        hgPbOk: 0
    sourceName: Korea Ocean Research & Development Institute
         taxId: 310752
*************************** 3. row ***************************
          name: calMil1
   description: Dec. 2013 (Callorhinchus_milii-6.1.3/calMil1)
       nibPath: /gbdb/calMil1
      organism: Elephant shark
    defaultPos: KI635875:1934002-2090480
        active: 1
      orderKey: 5525
        genome: Elephant shark
scientificName: Callorhinchus milii
      htmlPath: /gbdb/calMil1/html/description.html
      hgNearOk: 0
        hgPbOk: 0
    sourceName: Institute of Molecular and Cell Biology, Singapore
         taxId: 7868
    .....
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7.0 years ago

You can get an XML listing of all the current genomes from their DAS server: http://genome.ucsc.edu/cgi-bin/das/dsn

 $ curl -s http://genome.ucsc.edu/cgi-bin/das/dsn | head -n20

http://www.biodas.org/dtd/dasdsn.dtd">
<DASDSN>
   <DSN>
     <SOURCE id="hg38" version="1.00">Dec. 2013 (GRCh38/hg38) at UCSC</SOURCE>
     <DESCRIPTION>Human Dec. 2013 (GRCh38/hg38) Genome at UCSC</DESCRIPTION>
     <MAPMASTER>http://genome.cse.ucsc.edu:80/cgi-bin/das/hg38</MAPMASTER>
   </DSN>
   <DSN>
     <SOURCE id="hg19" version="1.00">Feb. 2009 (GRCh37/hg19) at UCSC</SOURCE>
     <DESCRIPTION>Human Feb. 2009 (GRCh37/hg19) Genome at UCSC</DESCRIPTION>
     <MAPMASTER>http://genome.cse.ucsc.edu:80/cgi-bin/das/hg19</MAPMASTER>
   </DSN>
   <DSN>
     <SOURCE id="hg18" version="1.00">Mar. 2006 (NCBI36/hg18) at UCSC</SOURCE>
     <DESCRIPTION>Human Mar. 2006 (NCBI36/hg18) Genome at UCSC</DESCRIPTION>
     <MAPMASTER>http://genome.cse.ucsc.edu:80/cgi-bin/das/hg18</MAPMASTER>
   </DSN>
   <DSN>
     <SOURCE id="hg17" version="1.00">May 2004 (NCBI35/hg17) at UCSC</SOURCE>
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The genomepy python library uses this method for listing UCSC genomes.

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