Interactive Genome Viewer (IGV)
IGV Hosted Reference Genomes
Interactive Genome Viewer (IGV)
IGV Hosted Reference Genomes
The IGV browser comes with many hosted options for common Reference Genomes to view Alignment Files to. Here is a list of the options provided.
| Id | Refernce Name | Fasta URL | Index URL | Supplementary Tracks |
|---|---|---|---|---|
| chm13v2.0 | Human (T2T CHM13-v2.0) | chm13v2.0.fa | chm13v2.0.fa.fai | CAT/Liftoff Genes, Augustus, Genes |
| chm13v1.1 | Human (T2T CHM13-v1.1) | GCA_009914755.3_CHM13_T2T_v1.1_genomic.fna | GCA_009914755.3_CHM13_T2T_v1.1_genomic.fna.fai | Annotations, Genes |
| hg38 | Human (GRCh38/hg38) | hg38.fa | hg38.fa.fai | Refseq Genes |
| hg38_1kg | Human (hg38 1kg/GATK) | GRCh38_full_analysis_set_plus_decoy_hla.fa | GRCh38_full_analysis_set_plus_decoy_hla.fa.fai | Refseq Genes |
| hg19 | Human (GRCh37/hg19) | hg19.fasta | hg19.fasta.fai | Refseq Genes |
| hg18 | Human (hg18) | hg18.fasta | hg18.fasta.fai | Refseq Genes |
| mm39 | Mouse (GRCm39/mm39) | mm39.fa | mm39.fa.fai | Refseq Genes |
| mm10 | Mouse (GRCm38/mm10) | mm10.fa | mm10.fa.fai | Refseq Genes |
| mm9 | Mouse (NCBI37/mm9) | mm9.fasta | mm9.fasta.fai | Refseq Genes, Genes |
| rn7 | Rat (rn7) | rn7.fa | rn7.fa.fai | Genes, Genes |
| rn6 | Rat (RGCS 6.0/rn6) | rn6.fa | rn6.fa.fai | Refseq Genes, Genes |
| gorGor6 | Gorilla (Kamilah_GGO_v0/gorGor6) | gorGor6.fa | gorGor6.fa.fai | Refseq Genes, Genes |
| gorGor4 | Gorilla (gorGor4.1/gorGor4) | gorGor4.fa | gorGor4.fa.fai | Refseq Genes |
| panTro6 | Chimp (panTro6) (panTro6) | panTro6.fa | panTro6.fa.fai | Refseq Genes, Genes |
| panTro5 | Chimp (panTro5) (panTro5) | panTro5.fa | panTro5.fa.fai | Refseq Genes, Genes |
| panTro4 | Chimp (SAC 2.1.4/panTro4) | panTro4.fa | panTro4.fa.fai | Refseq Genes, Genes |
| macFas5 | Macaca fascicularis (macFas5) | macFas5.fa | macFas5.fa.fai | Genes, Genes |
| GCA_011100615.1 | Macaca fascicularis 6.0 (GCA_011100615.1) | Macaca_fascicularis.Macaca_fascicularis_6.0.dna.toplevel.fa.gz | Macaca_fascicularis.Macaca_fascicularis_6.0.dna.toplevel.fa.gz.fai | Annotations, Genes |
| panPan2 | Bonobo (MPI-EVA panpan1.1/panPan2) | panPan2.fa | panPan2.fa.fai | Refseq Genes, Genes |
| canFam3 | Dog (Broad CanFam3.1/canFam3) | canFam3.fa | canFam3.fa.fai | Refseq Genes, Genes |
| canFam4 | Dog (UU_Cfam_GSD_1.0/canFam4) | canFam4.fa | canFam4.fa.fai | Genes |
| canFam5 | Dog (canFam5) | canFam5.fa | canFam5.fa.fai | Genes, Genes |
| bosTau9 | Cow (ARS-UCD1.2/bosTau9) | bosTau9.fa | bosTau9.fa.fai | Refseq Genes, Genes |
| bosTau8 | Cow (UMD_3.1.1/bosTau8) | bosTau8.fa | bosTau8.fa.fai | Refseq Genes, Genes |
| susScr11 | Pig (SGSC Sscrofa11.1/susScr11) | susScr11.fa | susScr11.fa.fai | Refseq Genes, Genes |
| galGal6 | Chicken (galGal6) | galGal6.fa | galGal6.fa.fai | NCBI Refseq Genes |
| GCF_016699485.2 | Gallus gallus (GCF_016699485.2) | GCF_016699485.2.fa | GCF_016699485.2.fa.fai | Genes, RefSeq Transcripts |
| danRer11 | Zebrafish (GRCZ11/danRer11) | danRer11.fa | danRer11.fa.fai | Refseq Genes, Genes |
| danRer10 | Zebrafish (GRCZ10/danRer10) | danRer10.fa | danRer10.fa.fai | Refseq Genes, Genes |
| ce11 | C. elegans (ce11) | ce11.fa | ce11.fa.fai | Refseq Genes |
| dm6 | D. melanogaster (dm6) | dm6.fa | dm6.fa.fai | Refseq Genes |
| dm3 | D. melanogaster (dm3) | dm3.fa | dm3.fa.fai | UCSC Refseq Genes |
| dmel_r5.9 | D. melanogaster (dmel_r5.9) | dmel-all-chromosome-r5.9.fasta | dmel-all-chromosome-r5.9.fasta.fai | Transcripts |
| sacCer3 | S. cerevisiae (sacCer3) | sacCer3.fa | sacCer3.fa.fai | Refseq Genes |
| ASM294v2 | S. pombe (ASM294v2) | Schizosaccharomyces_pombe_all_chromosomes.fa | Schizosaccharomyces_pombe_all_chromosomes.fa.fai | Pombase forward strand, Pombase reverse strand |
| ASM985889v3 | Sars-CoV-2 (ASM985889v3) | GCF_009858895.2_ASM985889v3_genomic.fna | GCF_009858895.2_ASM985889v3_genomic.fna.fai | Annotations |
| tair10 | A. thaliana (TAIR 10) | TAIR10_chr_all.fas | TAIR10_chr_all.fas.fai | Genes |
| GCA_003086295.2 | Peanut (GCA_003086295.2) | GCF_003086295.2_arahy.Tifrunner.gnm1.KYV3_genomic.fna | GCF_003086295.2_arahy.Tifrunner.gnm1.KYV3_genomic.fna.fai | Annotations |
| GCF_001433935.1 | O. sativa IRGSP-1.0 (GCF_001433935.1) | GCF_001433935.1_IRGSP-1.0_genomic.fna.gz | GCF_001433935.1_IRGSP-1.0_genomic.fna.gz.fai | MSU V7 genes |
| NC_016856.1 | Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S | NC_016856.1.fna | NC_016856.1.fna.fai | NC_016856.1.gff.gz |
| GCA_000182895.1 | Coprinopsis cinerea okayama7#130 (GCA_000182895.1) | GCA_000182895.1.fa | GCA_000182895.1.fa.fai | Gene models |
More info about these options can be found here.
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