Hosted Genomes

The IGV genome server hosts several genomes. See the section on loading genomes for instructions. Our thanks to the contributors.

Human

  • Source: UCSC Genome Bioinformatics, http://genome.ucsc.edu/
  • Assemblies:
    • UCSC hg19 (GCA_000001405.1), February 2009
    • UCSC hg18 (NCBI build 36.1), March 2006
    • UCSC hg17 (NCBI build 35), May 2004
    • UCSC hg16 (NCBI build 34), July 2003

Human: 1000 Genomes

Mouse (Mus musculus)

  • Source: UCSC Genome Bioinformatics, http://genome.ucsc.edu/
  • Assemblies:
    • UCSC mm9 (NCBI build 37), July 2007
    • UCSC mm8 (NCBI build 36), Febuary 2006
    • UCSC mm7 (NCBI build 35), August 2005

Acinetobacter baumannii

Anopheles Gambiae (African Malaria Mosquito)

Aplysia californica (Sea hare)

Arabidopsis thaliana

  • Source: The Arabidopsis Information Resource, http://www.arabidopsis.org/
  • Assemblies:
    • TAIR 8, November 2009
    • TAIR 9, March 2010
    • TAIR 10, November 2010

Aspergillus nidulans

  • Source: Aspergillus Comparative Sequencing Project, Broad Institute of Harvard and MIT (http://www.broadinstitute.org/)
  • Assembly: Aspergillus nidulans FGSC A4, July 2009

Autographa californica multiple nucleopolyhedrovirus

Banana

Bacillus Subtilis

Bordatella pertussis

C. elegans

C. savignyi

Chicken (Gallus gallus)

Chimpanzee (Pan troglodytes)

Clostridium thermocellum

Cow (Bos taurus)

D. discoideum (Slime mold)

Dog (Canis familiaris)

  • Source:  UCSC Genome Bioinformatics, http://genome.ucsc.edu/
  • Assemblies:
    • canFam2
    • canFam3
  • Lindblad-Toh K, et al. Genome sequence, comparative analysis and haplotype
    structure of the domestic dog. Nature. 2005 Dec 8;438:803-19

Drosophila melanogaster (Fruit fly)

Escherichia coli str. K-12 substr. MG1655 K12

Escherichia coli O157:H7 str. EDL933

  • Source:
    • NC_002655.2: ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_O157_H7_EDL933_uid57831/
    • Genbank : http://www.ncbi.nlm.nih.gov/nuccore/NC_002655

Enterobacteria phage phiX174 sensu lato

Frog (Xenopus tropicalis)

Giardia lamblia

  • Source: GiardiaDB, http://giardiadb.org/ (GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis.)
  • Assembly: Release 2.0, November 2009

Guinea Pig (Cavia porcellus)

Horse (Equus caballus)

Human Immunodeficiency Virus

Leishmania major (Friedlin strain)

Magnaporthe oryzae

Mycobacterium tuberculosis

Neisseria meningitidis

Neurospora crassa

Opossum (Monodelphis domestica)

Oryza sativa (Rice)

  • Source: Rice Genome Annotation Project, http://rice.plantbiology.msu.edu/
  • Assembly:
    • release 6, January 2009
    • release 6.1, June 2009
    • release 7, October 2011 (NOTE: The annotation GFF file for this assembly is very large.  You will need to start IGV with at least the 1.2 GB memory option, and preferably the 2.0 GB option, to work with this assembly.)

Physcomitrella patens

Pig (Sus scrofa)

Plasmodium falciparum

Plasmodium vivax

Rat (Rattus norvegicus)

Rabbit (Oryctolagus cuniculus)

Rhesus Macaque (Macaca mulatta)

Crab-Eating Macaque (Macaca fascicularis)

Salmonella Enterica

Sheep (Ovis aries)

Sea urchin (S. purpuratus)

Soybean (Glycine Max)

Stickleback (Gasterosteus aculeatus)

Tomato (Solanum lycopersicum)

Toxoplasma gondii 

Tribolium castaneum (Red flour beetle)

Trypanosoma brucei

Trypanosoma brucei gambiense

Vibrio cholerae

Yeast (Candida albicans)

Yeast (Saccharomyces cerevisiae)

Yeast (Schizosaccharomyces pombe)

Zea mays ssp. mays (Maize, Corn)

Zebra finch (Taeniopygia guttata)

Zebrafish (Danio rerio)

  • Source: UCSC Genome Bioinformatics, http://genome.ucsc.edu/
  • Assembly:
    • ZV7/danRer5, July 2007
    • ZV8/danRer6, December 2008
    • ZV9/danRer7, July 2010