Hosted Genomes

The IGV genome server hosts several genomes. To load a hosted genome into IGV, launch IGV and select the genome from the drop-down list in the tool bar. Our thanks to the contributors.

Human

• Source: UCSC Genome Bioninformatics, 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

• Source: 1000 Genomes, http://www.1000genomes.org/
• Assembly: b37, October 2009
• Assembly: b36 (1kg ref), December 2008

Mouse (Mus musculus)

• Source: UCSC Genome Bioninformatics, 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

Aplysia californica (Sea hare)

• Source: Broad Institute, http://www.broadinstitute.org/science/projects/mammals-models/vertebrates-invertebrates/aplysia/aplysia-genome-sequencing-project
• Assembly: Aplcal2.0

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

Bordatella pertussis

• Source: NCBI, ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Bordetella_pertussis_Tohama_I_uid57617/
• Assembly: Tohama I strain, accession PRJNA57617, refseq NC_002929.2

C. elegans

• Source: UCSC Genome Bioninformatics, http://genome.ucsc.edu/
• Assemblies:
  • UCSC ce6, May 2008
  • UCSC ce4, January 2007
• Source: WormBase, http://www.wormbase.org
• Assemblies:
  • WS201, March 2009
  • WS220, October 2010

C. savignyi

• Source: Stanford, http://mendel.stanford.edu/SidowLab/ciona.html
• Assemblies: 2.1, March 2006

Chicken (Gallus gallus)

• Source: UCSC Genome Bioninformatics, http://genome.ucsc.edu/
• Assembly: UCSC galGal3 (WUSTL v 2.1), May 2006

Chimpanzee (Pan troglodytes)

• Source: UCSC Genome Bioninformatics, http://genome.ucsc.edu/
• Assembly: UCSC panTro2 (CGSC v 2.1), March 2006

Clostridium thermocellum

• Source: NCBI, ftp://ftp.ncbi.nih.gov/genomes/Bacteria/
• Assembly: NC009012, Sep 2011

Cow (Bos taurus)

• Source: University of Maryland, http://www.cbcb.umd.edu/research/bos_taurus_assembly.shtml
  • Assembly: UMD 3.0
• Source: UCSC Genome Bioninformatics, http://genome.ucsc.edu/, originally developed by the Baylor College of Medicine Human Genome Sequencing Center (HGSC)
  • Assembly: Bos taurus 3 (Aug 2006; Baylor 3.1/bosTau3)
  • Assembly: Bos taurus 4 (Oct 2007; Baylor 4.0/bosTau4)
  • Assembly: Bos taurus 6 (Nov 2009; UMD 3.1/bosTau6)

D. discoideum (Slime mold)

• Source:  dictyBase, http://dictybase.org/
• Assembly: 05-13-2010

Dog (Canis familiaris)

• Source:  UCSC Genome Bioninformatics, http://genome.ucsc.edu/
• Assembly: canFam2
• 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)

• Source: UCSC Genome Bioninformatics, http://genome.ucsc.edu/
  • dm3, April 2006
  • dm2, April 2004
• Souce: FlyBase, http://flybase.org/
  • 5.9, June 2008
  • 5.22, October 2009
  • 5.33, February 2011

Escherichia coli str. K-12 substr. MG1655 K12

• Source:
  • NC_000913:  ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Escherichia_coli_K_12_substr__MG1655_uid57779/
  • Genbank U00096.2:  http://ecogene.org/index.php
• Versions: Genbank U00096.2,  RefSeq NC_000913
• References:

  • The complete genome sequence of Escherichia coli K-12.

    Blattner FR, Plunkett G 3rd, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y.  Science. 1997 Sep 5;277(5331):1453-62.

  • Escherichia coli K-12: a cooperatively developed annotation snapshot--2005.

    Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G 3rd, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL.  Nucleic Acids Res. 2006 Jan 5;34(1):1-9. Print 2006.

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

Frog (Xenopus tropicalis)

• Sources: Dept of Energy Joint Genome Institute, http://genome.jgi-psf.org/Xentr4/Xentr4.home.html
  and USCS, http://hgdownload.cse.ucsc.edu/downloads.html#xenTro
• Assembly: v 4.1 (also known as xenTro2) August 2005

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)

• Source: UCSC Genome Bioninformatics, http://genome.ucsc.edu
• Assembly: CavPor3, Feb. 2008, Broad Institute

Horse (Equus caballus)

• Source: UCSC Genome Bioninformatics, http://genome.ucsc.edu
• Assembly: equCab, Sep. 2007, Broad Institute

Leishmania major (Friedlin strain)

• Source: TriTrypDB
• Assemblies:
  • 2009-09-10
  • 4.0
• Reference: The genome of the kinetoplastid parasite, Leishmania major. Science 2005 Jul 15;309(5733):436-42 Ivens et al.

Magnaporthe oryzae

• Source: Broad Institute, http://www.broadinstitute.org/annotation/genome/magnaporthe_comparative/MultiHome.html
• Assembly: mg8

Neurospora crassa

• Source: Broad Institute, http://www.broadinstitute.org/annotation/genome/neurospora/Home.html
• Assembly: v3
• Assembly: OR74A (NC10)

Opossum (Monodelphis domestica)

• Source: UCSC Genome Bioninformatics, http://genome.ucsc.edu/
• Assembly: monDom5, October 2006

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

• Source: Physcome Project, http://www.cosmoss.org
• Assembly: Version 1.2,  October 2009
• Rensing SA, Lang D, Zimmer AD, et al, (70 co-authors). The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science (2008) 319:64–69

Pig (Sus scrofa)

• Source: Ensembl, http://www.ensembl.org/Sus_scrofa/Info/Index
• Assembly: 9.56, September 2009

Plasmodium falciparum

• Source: Wellcome Sanger Trust, http://www.sanger.ac.uk/Projects/P_falciparum/
  • 3D7 v2.1, February 2006
  • 3D7 v5.5
  • 3D7 v7.0
• Source: PlasmoDB, http://plasmodb.org/plasmo/
  • Version 6.1, September 2009

Plasmodium vivax

• Source: PlasmoDB, http://plasmodb.org/common/downloads/release-7.2/Pvivax/
  • Version 7.2, March 2011

Rat (Rattus norvegicus)

• Source: UCSC Genome Bioninformatics, http://genome.ucsc.edu/, based on version 3.4 produced by the Atlas group at Baylor Human Genome Sequencing Center (HGSC) as part of the Rat Genome Sequencing Consortium
  • UCSC Baylor 3.4/rn4 (Nov 2004)

Rhesus macaque (Macaca mulatta)

• Source: UCSC Genome Bioninformatics, http://genome.ucsc.edu/
• Assembly: UCSC rheMac2, January 2006

Sea urchin (S. purpuratus)

• Source (assembly): Human Genome Sequencing Center, Baylor College of Medicine (http://www.hgsc.bcm.tmc.edu/project-species-o-Strongylocentrotus purpuratus.hgsc?pageLocation=Strongylocentrotus purpuratus).
  • Spur_2.1 (Sep 2006)
  • Spur_2.5 (Feb 2010)
• Source (annotation): SpBase (http://www.spbase.org).
  • Release 4 (Oct 2009)
  • Release 5 (Jun 2010)

Stickleback (Gasterosteus aculeatus)

• Source: UCSC Genome Bioninformatics, http://genome.ucsc.edu/, from the Broad sequence
• Assembly: Broad Institute v1.0 (gasAcu1),  Feb 2006

Toxoplasma gondii 

• Source: http://toxodb.org/toxo/
  B. Gajria, A. Bahl, J. Brestelli, J. Dommer, S. Fischer, X. Gao, M. Heiges, J. Iodice, J. C. Kissinger, A. J. Mackey, et al. ToxoDB: an integrated Toxoplasma gondii database resource. Nucleic Acids Res., November 14, 2007; (2007). (http://nar.oxfordjournals.org/cgi/content/full/gkm981v1)
• Assembly: ME49

Tribolium castaneum (Red flour beetle)

• Source: Human Sequencing Genome Center at Baylor University, http://www.hgsc.bcm.tmc.edu/projects/tribolium/
• Assemblies:
  • TCas V2
  • TCas V3

Trypanosoma brucei TREU927

• Source: TriTrypDB
• Versions: 2009-10-06, 4.0
• Reference: The genome of the African trypanosome Trypanosoma brucei. Science 2005 Jul 15;309(5733):416-22 Berriman et al.

Trypanosoma brucei gambiense

• Source: TriTrypDB
• Versions: 2009-09-07 (2.5), 4.0
• Reference: The genome sequence of Trypanosoma brucei gambiense, causative agent of chronic human african trypanosomiasis. PLos Negl Trop Dis. 2010 Apr 13;4(4) Jackson et. al.

Yeast (Candida albicans)

• Source: UCSC Genome Bioninformatics, http://www.candidagenome.org/
• Assembly: 21 (strain SC5314), April 2007

Yeast (Saccharomyces cerevisiae)

• Source: UCSC Genome Bioninformatics, http://genome.ucsc.edu/
  • Assemblies:
    • sacCer1, October 2003
    • sacCer2, June 2008
• Source: Wellcome Trust Sanger Institute, http://www.sanger.ac.uk/research/projects/genomeinformatics/sgrp.html
  • Assembly: sk1, February 2008
  • Assembly: Y55
• Source: Saccharomyces Genome Database, http://www.yeastgenome.org/
  • Assembly: EF3 r62, April 2011
• Source: GEO, http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GSM552910
  • Assembly: GSM552910, June 2010

Yeast (Schizosaccharomyces pombe)

• Source: Wellcome Trust Sanger Institute, http://www.sanger.ac.uk/Projects/S_pombe/
• Assemblies:
  • July 2009
  • EF 1.55

Zea mays ssp. mays (Maize, Corn)

• Source: Maize Genome Sequencing Project, http://www.maizesequence.org/index.html
• Assembly: B73 (4a.53), November 2009

Zebra finch (Taeniopygia guttata)

• Source: UCSC Genome Bioninformatics, http://genome.ucsc.edu/
• Assembly: taeGut1, July 2008

Zebrafish (Danio rerio)

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