Reference Genomes

The following reference genomes are available at /panfs/roc/rissdb/genomes, and also in Galaxy unless noted otherwise.

Species (common) Species (latin) Build (rissdb) Galaxy Name Source
Apple Malus_domestica Malus_domestica1 Apple Malus x domestica V1.0 (Malus_domestica1) GDR
Arabidopsis Arabidopsis_thaliana araTha_tair9 Arabidopsis thaliana (TAIR) (araTha_tair9) Ensembl
Arabidopsis Arabidopsis_thaliana Arabidopsis_thaliana_TAIR10 Arabidopsis thaliana TAIR10 (Arabidopsis_thaliana_TAIR10) Ensembl
Arabidopsis Arabidopsis_thaliana TAIR10 TAIR10  
Bacteria Streptomyces_clavuligerus Streptomyces_clavuligerus Not in Galaxy  
Bovine TB Mycobacterium_bovis MBO_bovis Not in Galaxy  
Bread yeast Saccharomyces_cerevisiae sacCer2 S. cerevisiae June 2008 (SGD/sacCer2) (sacCer2) UCSC
Brome grass Brachypodium_distachyon brachy1.0 Brachypodium_distachyon brome grass (brachy1.0) JGI
Candida albicans Candida_albicans C_albicans_SC5314 Candida albicans SC5314, Assembly 21 A21 (C_albicans_SC5314) CGD
Carolina anole Anolis_carolinensis anoCar2 anoCar2  
Cat Felis_catus felCat3 Cat Mar. 2006 (Broad/felCat3) (felCat3) UCSC
Chicken Gallus_gallus galGal3 Chicken May 2006 (WUGSC 2.1/galGal3) (galGal3) UCSC
Chimp Pan_troglodytes panTro2 Chimp Mar. 2006 (CGSC 2.1/panTro2) (panTro2) UCSC
Chlamydomonas Chlamydomonas_reinhardtii Chlre4 Chlamydomonas reinhardtii 2007 Oct 12 (JGI) (Chlre4)  
Chlamydomonas Cryptococcus_neoformans Cryptococcus_neoformans_grubii_H99 Cryptococcus neoformans var. grubii H99 Broad
Corn Zea_mays Zmays_121 Zea mays (maize) (JGI phytozome v6 121) (Zmays_121) JGI
Corn Zea_mays ZmB73v2 Zea mays (maize) (MaizeSequence.org ZmB73_v2) (ZmB73v2)  
Corn smut Ustilago_maydis Ustilago_maydis1 Ustilago maydis (corn smut) (MIPS MUMBY - Broad) (Ustilago_maydis1) MIPS
Cow Bos_taurus Bos_taurus_UMD_3.1 Cow (CBCB August 2009) (Bos_taurus_UMD_3.1) UMD
Cow Bos_taurus bosTau4 Cow Oct. 2007 (Baylor 4.0/bosTau4) (bosTau4) UCSC
Dog Canis_lupus canFam2 Dog May 2005 (Broad/canFam2) (canFam2) UCSC
Dog Canis_lupus canFam3_canonical canFam3_canonical  
Dog Canis_lupus canFam3 Dog Sep. 2011 (Broad CanFam3.1/canFam3) (canFam3)  
E coli Escherichia_coli eschColi_K12 Escherichia coli K12 (Escherichia coli K12 substr. MG1655) (eschColi_K12) NCBI
Fruitfly Drosophilia_melanogaster dm3 D. melanogaster Apr. 2006 (BDGP R5/dm3) (dm3) UCSC
Fusarium Fusarium_oxysporum Fusarium_oxysporum18813 Not in Galaxy NCBI
Fusarium Fusarium_oxysporum F_oxysporum4287 Fusarium oxysporum f. sp. lycopersici 4287 F_oxysporum4287  
Fusarium Fusarium_verticillioides Fusarium_verticillioides15553 Gibberella moniliformis 7600 (NCBI genomeprj/15553 Broad) (Fusarium_verticillioides15553) NCBI
Fusarium Fusarium_graminearum Fusarium_graminearum243 Gibberella zeae PH-1 (NCBI genomeprj/243 Broad) (Fusarium_graminearum243) NCBI
Fusarium Fusarium_solani Fusarium_solani_Necha2 Nectria haematococca August 2009 (JGI) (Fusarium_solani_Necha2) JGI
Honeybee Apis_mellifera apiMel3 A. mellifera A. mellifera (Baylor HGSC Amel_3.0) (apiMel3) UCSC
Honeybee Apis_mellifera amel_4.5 Not in Galaxy  
Horse Equus_ferus equCab2 Horse Sep. 2007 (Broad/equCab2) (equCab2) UCSC
Human Homo_sapiens hg19 Human Feb. 2009 (GRCh37/hg19) (hg19) UCSC
Human Homo_sapiens hg19_canonical Human hg19 in GATK canonical chr order (no unknown or random) (hg19_canonical)  
Human Homo_sapiens hg18 Human Mar. 2006 (NCBI36/hg18) (hg18) UCSC
Human Homo_sapiens hg17 Human May 2004 (NCBI35/hg17) (hg17)  
Human Homo_sapiens GRCh37 Not in Galaxy  
Human Homo_sapiens hg19-chr19 Human hg19 chr19  
Lactic acid bacteria Enterococcus_faecalis efaec_OG1RF Not in Galaxy  
Mosquito Anopheles_gambiae AgamP3 AgamP3 Ensembl
Mouse Mus_musculus mm8 Mouse Feb. 2006 (NCBI36/mm8) (mm8) UCSC
Mouse Mus_musculus mm9 Mouse July 2007 (NCBI37/mm9) (mm9) UCSC
Mouse Mus_musculus mm9_canonical Mouse mm9 in GATK canonical chr order (no unknown or random) (mm9_canonical)  
Mouse Mus_musculus mm10 Not in Galaxy  
Mouse Mus_musculus mm10_canonical Mouse (Mus musculus) mm10_canonical  
Mouse Mus_musculus NCBIM37 Not in Galaxy  
Opossum Monodelphis_domestica monDom5 Opossum Oct. 2006 (Broad/monDom5) (monDom5) UCSC
Orangutan Pongo_abelii ponAbe2 Orangutan July 2007 (WUGSC 2.0.2/ponAbe2) (ponAbe2)  
Pig Sus_scrofa susScr3 susScr3  
Pig Sus_scrofa susScr2 Pig Nov. 2009 (SGSC Sscrofa9.2/susScr2) (susScr2) UCSC
Pig Sus_scrofa Sscrofa10 Pig Sep. 2010 (TGAC) (Sscrofa10) TGAC
Pig Sus_scrofa Sscrofa10.2 Pig Sep. 2011 (NCBI) (Sscrofa10.2) NCBI
Poplar Populus_trichocarpa Ptrichocarpa_156 Populus trichocarpa (Western poplar) (JGI assembly v2) (Ptrichocarpa_156) JGI
Potato Solanum_tuberosum Stuberosum_DM_v3_2.1.9 Not in Galaxy  
Potato Solanum_tuberosum Stuberosum_DM_v3-chr05 Potato S. tuberosum Group Phureja DM1-3 516R44 (CIP801092) Version 3 DM chromosome 5(Stuberosum_DM_v3-chr05)
Potato Solanum_tuberosum Stuberosum_DM_v3 Potato S. tuberosum Group Phureja DM1-3 516R44 (CIP801092) Version 3 DM (Stuberosum_DM_v3) MSU
Pufferfish Trubripes_Fugu fr2 Fugu Oct. 2004 (JGI 4.0/fr2) (fr2) UCSC
Rabbit Oryctolagus_cuniculus oryCun2 Rabbit Apr. 2009 (Broad/oryCun2) (oryCun2) UCSC
Rat Rattus_norvegicus rn4 Rat Nov. 2004 (Baylor 3.4/rn4) (rn4) UCSC
Red bread mold Neospora_crassa NcrassaOR74A_NC12 NcrassaOR74A_NC12  
Rhesus monkey Rhesus_macaque rheMac3 Rhesus Oct. 2010 (BGI CR_1.0/rheMac3)(rheMac3)  
Rice Oryza_sativa Oindica_Jan2005 Rice Oryza sativa indica (Oindica_Jan2005) Ensembl
Rice Oryza_sativa Osativa_MSU6 Rice Oryza sativa japonica Jan 2009 (Osativa_MSU6) Ensembl
Roundworm Caenorhabditis_elegans WS200 C. elegans Feb 2009 (WS200/ce7) (ce7) Ensembl
Roundworm Caenorhabditis_elegans WS190 C. elegans May 2008 (WS190/ce6) (WS190)  
Roundworm Caenorhabditis_elegans WS220 C. elegans Oct 2010 (WS220)  
Roundworm Caenorhabditis_elegans ce10 C. elegans Oct 2010 (WS220/ce10) (ce10)  
Roundworm Caenorhabditis_elegans WS236 WS236  
Silkworm Bombyx_mori bombyx_2_0 Not in Galaxy  
Soybean Glycine_max Gmax_109 Glycine max Soybean (JGI phytozome v6 109) (Gmax_109) JGI
Thale cress Medicago_truncatula Mtruncatula_135 Medicago truncatula Thale cress (JGI phytozome v6 135) (Mtruncatula_135) JGI
Tomato Solanum_lycopersicum SL_2_4 Not in Galaxy  
Turkey Meleagris_gallopavo Turkey_2.01 Meleagris gallopavo Nicholas (Turkey_2.01) Ensembl
Western clawed frog Xenopus_tropicalis xenTro2 X. tropicalis Aug. 2005 (JGI 4.1/xenTro2) (xenTro2) UCSC
Zebra finch Taeniopygia_guttata taeGut1 Zebra finch Jul. 2008 (WUGSC 3.2.4/taeGut1) (taeGut1) UCSC
Zebra fish Danio_rerio danRer6 Zebrafish Dec. 2008 (Zv8/danRer6) (danRer6) UCSC