General references and annotations

Arabidopsis thaliana (TAIR10.52)

Common name Thale cress
Assembly TAIR10
Ensembl release 52
Reference sequence https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-52/fasta/arabidopsis_thaliana/dna/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa.gz
Ensembl annotations https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-52/gff3/arabidopsis_thaliana/Arabidopsis_thaliana.TAIR10.52.gff3.gz

Avena sativa (Oat_OT3098_v2.61)

Common name Oat
Assembly Oat_OT3098_v2
Ensembl release 61
Reference sequence https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-61/fasta/avena_sativa_ot3098/dna/ (files Avena_sativa_ot3098.Oat_OT3098_v2.dna.chromosome.*.fa.gz, where * is 1A, 1C, 1D, 2A, 2C, 2D, 3A, 3C, 3D, 4A, 4C, 4D, 5A, 5C, 5D, 6A, 6C, 6D, 7A, 7C, 7D)
Ensembl annotations https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-61/gff3/avena_sativa_sang/Avena_sativa_sang.Asativa_sang.v1.1.61.gff3.gz

Bos taurus (ARS-UCD1.2.105) (legacy)

Common name Cow
Assembly ARS-UCD1.2
Ensembl release 105
Reference sequence https://ftp.ensembl.org/pub/release-105/fasta/bos_taurus/dna/ (files Bos_taurus.ARS-UCD1.2.dna.primary_assembly.*.fa.gz, where * is 1-29, X, MT)
Ensembl annotations https://ftp.ensembl.org/pub/release-105/gff3/bos_taurus/Bos_taurus.ARS-UCD1.2.105.chr.gff3.gz

Bos taurus (ARSUCD2.0.114)

Common name Cow
Assembly ARS-UCD2.0
Ensembl release 114
Reference sequence https://ftp.ensembl.org/pub/release-114/fasta/bos_taurus/dna/ (files Bos_taurus.ARS-UCD2.0.dna.primary_assembly.*.fa.gz, where * is 1-29, X, Y, MT)
Ensembl annotations https://ftp.ensembl.org/pub/release-114/gff3/bos_taurus/Bos_taurus.ARS-UCD2.0.114.chr.gff3.gz

Caenorhabditis elegans (WBcel235.105)

Common name Roundworm
Assembly WBcel235
Ensembl release 105
Reference sequence https://ftp.ensembl.org/pub/release-105/fasta/caenorhabditis_elegans/dna/Caenorhabditis_elegans.WBcel235.dna_sm.toplevel.fa.gz
Ensembl annotations https://ftp.ensembl.org/pub/release-105/gff3/caenorhabditis_elegans/Caenorhabditis_elegans.WBcel235.105.gff3.gz

Canis lupus familiaris (ROS_Cfam_1.0.105)

Common name Dog (labrador retriever breed)
Assembly ROS_Cfam_1.0
Ensembl release 105
Reference sequence https://ftp.ensembl.org/pub/release-105/fasta/canis_lupus_familiaris/dna/ (files Canis_lupus_familiaris.ROS_Cfam_1.0.dna.primary_assembly.*.fa.gz, where * is 1-38, X, Y)
Ensembl annotations https://ftp.ensembl.org/pub/release-105/gff3/canis_lupus_familiaris/Canis_lupus_familiaris.ROS_Cfam_1.0.105.chr.gff3.gz

Capra hircus (ARS1.114)

Common name Goat
Assembly ARS1
Ensembl release 114
Reference sequence https://ftp.ensembl.org/pub/release-114/fasta/capra_hircus/dna/ (files Capra_hircus.ARS1.dna.chromosome.*.fa.gz, where * is 1-29, MT)
Ensembl annotations https://ftp.ensembl.org/pub/release-114/gff3/capra_hircus/Capra_hircus.ARS1.114.chr.gff3.gz

Danio rerio (GRCz11.10.105)

Common name Zebra fish
Assembly GRCz11.10
Ensembl release 105
Reference sequence https://ftp.ensembl.org/pub/release-105/fasta/danio_rerio/dna/ (files Danio_rerio.GRCz11.dna.chromosome.*.fa.gz, where * is 1-25, MT)
Ensembl annotations https://ftp.ensembl.org/pub/release-105/gff3/danio_rerio/Danio_rerio.GRCz11.105.chr.gff3.gz

Drosophila melanogaster (BDGP6.32.105)

Common name Fruit fly
Assembly BDGP6.32
Ensembl release 105
Reference sequence https://ftp.ensembl.org/pub/release-105/fasta/drosophila_melanogaster/dna/ (files Drosophila_melanogaster.BDGP6.32.dna.primary_assembly.*.fa.gz, where * is 2L, 2R, 3L, 3R, 4, X, Y, mitochondrion_genome)
Ensembl annotations https://ftp.ensembl.org/pub/release-105/gff3/drosophila_melanogaster/Drosophila_melanogaster.BDGP6.32.105.chr.gff3.gz

Equus caballus (EquCab3.0.105)

Common name Horse
Assembly EquCab3.0
Ensembl release 105
Reference sequence https://ftp.ensembl.org/pub/release-105/fasta/equus_caballus/dna/ (files Equus_caballus.EquCab3.0.dna.primary_assembly.*.fa.gz, where * is 1-31, X)
Ensembl annotations https://ftp.ensembl.org/pub/release-105/gff3/equus_caballus/Equus_caballus.EquCab3.0.105.chr.gff3.gz

Felis catus (F.catus_Fca126_mat1.0.114)

Common name Domestic cat
Assembly Fca126_mat1.0
Ensembl release 114
Reference sequence https://ftp.ensembl.org/pub/release-114/fasta/felis_catus/dna/ (files Felis_catus.F.catus_Fca126_mat1.0.dna.primary_assembly.*.fa.gz, where * is A1, A2, A3, B1, B2, B3, B4, C1, C2, D1, D2, D3, D4, E1, E2, E3, F1, F2, X)
Ensembl annotations https://ftp.ensembl.org/pub/release-114/gff3/felis_catus/Felis_catus.F.catus_Fca126_mat1.0.114.chr.gff3.gz

Gallus gallus (GRCg7b.110)

Common name Chicken
Assembly GRCg7b
Ensembl release 110
Reference sequence https://ftp.ensembl.org/pub/release-110/fasta/gallus_gallus/dna/ (files Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.dna.primary_assembly.*.fa.gz, where * is 1-39, W, Z, MT)
Ensembl annotations https://ftp.ensembl.org/pub/release-110/gff3/gallus_gallus/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.110.gff3.gz

Gasterosteus aculeatus (GAculeatus_UGA_version5.112)

Common name Three-spined stickleback
Assembly GAculeatus_UGA_version5
Ensembl release 112
Reference sequence https://ftp.ensembl.org/pub/release-112/fasta/gasterosteus_aculeatus/dna/ (files Gasterosteus_aculeatus.GAculeatus_UGA_version5.dna.primary_assembly.*.fa.gz, where * is I, II, III, IV, IX, V, VI, VII, VIII, X, XI, XII, XIII, XIV, XIX, XV, XVI, XVII, XVIII, XX, XXI, Y)
Ensembl annotations https://ftp.ensembl.org/pub/release-112/gff3/gasterosteus_aculeatus/Gasterosteus_aculeatus.GAculeatus_UGA_version5.112.gff3.gz

Glycine max (Glycine_max_v2.1.61)

Common name Soybean
Assembly Glycine_max_v2.1
Ensembl release 61
Reference sequence https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-61/fasta/glycine_max/dna/ (files Glycine_max.Glycine_max_v2.1.dna.chromosome.*.fa.gz, where * is 1-20)
Ensembl annotations https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-61/gff3/glycine_max/Glycine_max.Glycine_max_v2.1.61.chr.gff3.gz

Homo sapiens (GRCh38.103)

Common name Human
Assembly GRCh38.p13
Ensembl release 103
Reference sequence https://ftp.ensembl.org/pub/release-103/fasta/homo_sapiens/dna/ (files Homo_sapiens.GRCh38.dna.chromosome.*.fa.gz, where * is 1-22, MT, X, Y)
Ensembl annotations https://ftp.ensembl.org/pub/release-103/gff3/homo_sapiens/Homo_sapiens.GRCh38.103.chr.gff3.gz

Homo sapiens (GRCh38.noalt.106)

Common name Human
Assembly GRCh38
Ensembl release 106
Reference sequence https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz
Ensembl annotations https://ftp.ensembl.org/pub/release-106/gff3/homo_sapiens/Homo_sapiens.GRCh38.106.chr.gff3.gz

Hordeum vulgare (MorexV3_pseudomolecules_assembly.61)

Common name Barley
Assembly MorexV3_pseudomolecules_assembly
Ensembl release 61
Reference sequence https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-61/fasta/hordeum_vulgare/dna/ (files Hordeum_vulgare.MorexV3_pseudomolecules_assembly.dna.primary_assembly.*.fa.gz, where * is 1H, 2H, 3H, 4H, 5H, 6H, 7H)
Ensembl annotations https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-61/gff3/hordeum_vulgare/Hordeum_vulgare.MorexV3_pseudomolecules_assembly.61.chr.gff3.gz

Macaca fascicularis (Macaca_fascicularis_6.0.105)

Common name Crab-eating macaque
Assembly Macaca_fascicularis_6.0
Ensembl release 105
Reference sequence https://ftp.ensembl.org/pub/release-105/fasta/macaca_fascicularis/dna/ (files Macaca_fascicularis.Macaca_fascicularis_6.0.dna.primary_assembly.*.fa.gz, where * is 1-20, X)
Ensembl annotations https://ftp.ensembl.org/pub/release-105/gff3/macaca_fascicularis/Macaca_fascicularis.Macaca_fascicularis_6.0.105.chr.gff3.gz

Macaca mulatta (Mmul_10.105)

Common name Rhesus macaque
Assembly Macaca_mulatta.Mmul_10
Ensembl release 105
Reference sequence https://ftp.ensembl.org/pub/release-105/fasta/macaca_mulatta/dna/ (files Macaca_mulatta.Mmul_10.dna.primary_assembly.*.fa.gz, where * is 1-20, X, Y, MT)
Ensembl annotations https://ftp.ensembl.org/pub/release-105/gff3/macaca_mulatta/Macaca_mulatta.Mmul_10.105.chr.gff3.gz

Mus musculus (GRCm38.101) (legacy)

Common name Mouse
Assembly GRCm38.p6
Ensembl release 101
Reference sequence https://ftp.ensembl.org/pub/release-101/fasta/mus_musculus/dna/ (files Mus_musculus.GRCm38.dna.chromosome.*.fa.gz, where * is 1-19, MT, X, Y)
Ensembl annotations https://ftp.ensembl.org/pub/release-101/gff3/mus_musculus/Mus_musculus.GRCm38.101.chr.gff3.gz

Mus musculus (GRCm39.114)

Common name Mouse
Assembly GRCm39
Ensembl release 114
Reference sequence https://ftp.ensembl.org/pub/release-114/fasta/mus_musculus/dna/ (files Mus_musculus.GRCm39.dna.chromosome.*.fa.gz, where * is 1-19, MT, X, Y)
Ensembl annotations https://ftp.ensembl.org/pub/release-114/gff3/mus_musculus/Mus_musculus.GRCm39.114.chr.gff3.gz

Oncorhynchus mykiss (Omyk_1.0.105)

Common name Rainbow trout
Assembly Omyk_1.0
Ensembl release 105
Reference sequence https://ftp.ensembl.org/pub/release-105/fasta/oncorhynchus_mykiss/dna/ (files Oncorhynchus_mykiss.Omyk_1.0.dna.primary_assembly.*.fa.gz, where * is 1-29)
Ensembl annotations https://ftp.ensembl.org/pub/release-105/gff3/oncorhynchus_mykiss/Oncorhynchus_mykiss.Omyk_1.0.105.chr.gff3.gz

Oncorhynchus mykiss (USDA_OmykA_1.1.114

Common name Rainbow trout
Assembly USDA_OmykA_1.1
Ensembl release 114
Reference sequence https://ftp.ensembl.org/pub/release-114/fasta/oncorhynchus_mykiss/dna/ (files Oncorhynchus_mykiss.USDA_OmykA_1.1.dna.primary_assembly.*.fa.gz, where * is 1-32, Y)
Ensembl annotations https://ftp.ensembl.org/pub/release-114/gff3/oncorhynchus_mykiss/Oncorhynchus_mykiss.USDA_OmykA_1.1.114.chr.gff3.gz

Oryctolagus cuniculus (OryCun2.0.105)

Common name Rabbit
Assembly OryCun2.0
Ensembl release 105
Reference sequence https://ftp.ensembl.org/pub/release-105/fasta/oryctolagus_cuniculus/dna/ (files Oryctolagus_cuniculus.OryCun2.0.dna.chromosome.*.fa.gz, where * is 1-21, X, MT)
Ensembl annotations https://ftp.ensembl.org/pub/release-105/gff3/oryctolagus_cuniculus/Oryctolagus_cuniculus.OryCun2.0.105.chr.gff3.gz

Oryza sativa (IRGSP-1.0.61)

Common name Rice
Assembly IRGSP-1.0
Ensembl release 61
Reference sequence https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-61/fasta/oryza_sativa/dna/ (files oryza_sativa/dna/Oryza_sativa.IRGSP-1.0.dna.chromosome.*.fa.gz, where * is 1-12, Mt, Pt)
Ensembl annotations https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-61/gff3/oryza_sativa/Oryza_sativa.IRGSP-1.0.61.chr.gff3.gz

Ovis aries (Rambouillet) (ARS-UI_Ramb_v2.0.114)

Common name Sheep (rambouillet breed)
Assembly ARS-UI_Ramb_v2.0
Ensembl release 114
Reference sequence https://ftp.ensembl.org/pub/release-114/fasta/ovis_aries_rambouillet/dna/ (files Ovis_aries_rambouillet.ARS-UI_Ramb_v2.0.dna.primary_assembly.*.fa.gz, where * is 1-26, MT, X)
Ensembl annotations https://ftp.ensembl.org/pub/release-114/gff3/ovis_aries_rambouillet/Ovis_aries_rambouillet.ARS-UI_Ramb_v2.0.114.chr.gff3.gz

Rattus norvegicus (mRatBN7.2.110)

Common name Rat
Assembly mRatBN_7.2
Ensembl release 110
Reference sequence https://ftp.ensembl.org/pub/release-110/fasta/rattus_norvegicus/dna/ (files Rattus_norvegicus.mRatBN7.2.dna.primary_assembly.*.fa.gz, files * is 1-20, MT, X, Y)
Ensembl annotations https://ftp.ensembl.org/pub/release-110/gff3/rattus_norvegicus/Rattus_norvegicus.mRatBN7.2.110.chr.gff3.gz

Rattus norvegicus (GRCr8.114)

Common name Rat
Assembly GRCr8
Ensembl release 114
Reference sequence https://ftp.ensembl.org/pub/release-114/fasta/rattus_norvegicus/dna/ (files Rattus_norvegicus.GRCr8.dna.primary_assembly.*.fa.gz, files * is 1-20, MT, X, Y)
Ensembl annotations https://ftp.ensembl.org/pub/release-114/gff3/rattus_norvegicus/Rattus_norvegicus.GRCr8.114.chr.gff3.gz

Saccharomyces cerevisiae (R64-1-1.105)

Common name Baker's yeast, brewer's yeast, budding yeast
Assembly R64-1-1
Ensembl release 105
Reference sequence https://ftp.ensembl.org/pub/release-105/fasta/saccharomyces_cerevisiae/dna/ (files Saccharomyces_cerevisiae.R64-1-1.dna.chromosome.*.fa.gz, where * is I, II, III, IV, IX, V, VI, VII, VIII, X, XI, XII, XIII, XIV, XV, XVI, Mito)
Ensembl annotations https://ftp.ensembl.org/pub/release-105/gff3/saccharomyces_cerevisiae/Saccharomyces_cerevisiae.R64-1-1.105.gff3.gz

Schizosaccharomyces pombe (ASM294v2.52)

Common name Fission yeast
Assembly ASM294v2
Ensembl release 52
Reference sequence https://ftp.ensemblgenomes.ebi.ac.uk/pub/fungi/release-52/fasta/schizosaccharomyces_pombe/dna/ (files Schizosaccharomyces_pombe.ASM294v2.dna.chromosome.*.fa.gz, where * is I, II, III, MT)
Ensembl annotations https://ftp.ensemblgenomes.ebi.ac.uk/pub/fungi/release-52/gff3/schizosaccharomyces_pombe/Schizosaccharomyces_pombe.ASM294v2.52.chr.gff3.gz

Secale cereale (Rye_Lo7_2018_v1p1p1.61)

Common name Rye
Assembly Rye_Lo7_2018_v1p1p1
Ensembl release 61
Reference sequence https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-61/fasta/secale_cereale/dna/ (files Secale_cereale.Rye_Lo7_2018_v1p1p1.dna.primary_assembly.*.fa.gz, where * is 0R, 1R, 2R, 3R, 4R, 5R, 6R, 7R)
Ensembl annotations https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-61/gff3/secale_cereale/Secale_cereale.Rye_Lo7_2018_v1p1p1.61.gff3.gz

Solanum tuberosum (SolTub_3.0.61)

Common name Potato
Assembly SolTub_3.0
Ensembl release 61
Reference sequence https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-61/fasta/solanum_tuberosum/dna/ (files Solanum_tuberosum.SolTub_3.0.dna.chromosome.*.fa.gz, where * is 1-12)
Ensembl annotations https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-61/gff3/solanum_tuberosum/Solanum_tuberosum.SolTub_3.0.61.chr.gff3.gz

Sorghum bicolor (Sorghum_bicolor_NCBIv3.61)

Common name Sorghum
Assembly Sorghum_bicolor_NCBIv3
Ensembl release 61
Reference sequence https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-61/fasta/sorghum_bicolor/dna/ (files Sorghum_bicolor.Sorghum_bicolor_NCBIv3.dna.chromosome.*.fa.gz, where * is 1-10)
Ensembl annotations https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-61/gff3/sorghum_bicolor/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.61.chr.gff3.gz

Sus scrofa (Sscrofa11.1.105)

Common name Pig
Assembly Sscrofa11.1
Ensembl release 105
Reference sequence https://ftp.ensembl.org/pub/release-105/fasta/sus_scrofa/dna/ (files Sus_scrofa.Sscrofa11.1.dna.chromosome.*.fa.gz, where * is 1-18, X, Y, MT)
Ensembl annotations https://ftp.ensembl.org/pub/release-105/gff3/sus_scrofa/Sus_scrofa.Sscrofa11.1.105.chr.gff3.gz

Sus scrofa (Triticum aestivum (IWGSC.61)

Common name Wheat
Assembly IWGSC
Ensembl release 61
Reference sequence https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-61/fasta/triticum_aestivum/dna/ (files Triticum_aestivum.IWGSC.dna.chromosome.*.fa.gz, where * is 1A, 1B, 1D, 2A, 2B, 2D, 3A, 3B, 3D, 4A, 4B, 4D, 5A, 5B, 5D, 6A, 6B, 6D, 7A, 7B, 7D, Un)
Ensembl annotations https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-61/gff3/triticum_aestivum/Triticum_aestivum.IWGSC.61.gff3.gz

Zea mays (Zm-B73-REFERENCE-NAM-5.0.57)

Common name Maize
Assembly Zm-B73-REFERENCE-NAM-5.0
Ensembl release 57
Reference sequence https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-57/fasta/zea_mays/dna/ (files Zea_mays.Zm-B73-REFERENCE-NAM-5.0.dna.chromosome.*.fa.gz, where * is 1-10, nonchromosomal)
Ensembl annotations https://ftp.ebi.ac.uk/ensemblgenomes/pub/release-57/plants/gff3/zea_mays/Zea_mays.Zm-B73-REFERENCE-NAM-5.0.57.chr.gff3.gz

Retired references and annotations

Retired reference genomes remain accessible only in projects that already contain samples associated with them. In such projects, it will still be possible to create new samples using the same sample kit-reference genome combination as the existing samples.

Gallus gallus (GRCg6a.105) (legacy)

Common name Chicken
Assembly GRCg6a
Ensembl release 105
Reference sequence https://ftp.ensembl.org/pub/release-105/fasta/gallus_gallus/dna/ (files Gallus_gallus.GRCg6a.dna.chromosome.*.fa.gz, where * is 1-33, W, Z, MT)
Ensembl annotations https://ftp.ensembl.org/pub/release-105/gff3/gallus_gallus/Gallus_gallus.GRCg6a.105.chr.gff3.gz

Rattus norvegicus (Rnor6.0.103) (legacy)

Common name Rat
Assembly Rnor_6.0
Ensembl release 103
Reference sequence https://ftp.ensembl.org/pub/release-103/fasta/rattus_norvegicus/dna/ (files Rattus_norvegicus.Rnor_6.0.dna.chromosome.*.fa.gz, where * is 1-20, MT, X, Y)
Ensembl annotations https://ftp.ensembl.org/pub/release-103/gff3/rattus_norvegicus/Rattus_norvegicus.Rnor_6.0.103.chr.gff3.gz