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update genomes
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@jrobinso
jrobinso committed Aug 22, 2024
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Showing 1 changed file with 81 additions and 100 deletions.
181 changes: 81 additions & 100 deletions resources/genomes.json
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Original file line number Diff line number Diff line change
Expand Up @@ -81,6 +81,7 @@
"aliasURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/chromAlias.txt.gz",
"twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit",
"chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes",
"chromosomeOrder": "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY",
"tracks": [
{
"name": "Refseq Genes",
Expand All @@ -89,8 +90,7 @@
"order": 1000001,
"infoURL": "https://www.ncbi.nlm.nih.gov/gene/?term=$$"
}
],
"chromosomeOrder": "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY"
]
},
{
"id": "hg38_1kg",
Expand Down Expand Up @@ -164,7 +164,7 @@
"cytobandURL": "https://hgdownload.soe.ucsc.edu/goldenPath/mm39/database/cytoBandIdeo.txt.gz",
"aliasURL": "https://hgdownload.soe.ucsc.edu/goldenPath/mm39/bigZips/mm39.chromAlias.txt",
"twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/mm39/bigZips/mm39.2bit",
"chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/mm39/database/chromInfo.txt.gz",
"chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/mm39/bigZips/mm39.chrom.sizes",
"tracks": [
{
"name": "Refseq Genes",
Expand Down Expand Up @@ -222,23 +222,16 @@
"fastaURL": "https://s3.amazonaws.com/igv.org.genomes/rn7/rn7.fa",
"indexURL": "https://s3.amazonaws.com/igv.org.genomes/rn7/rn7.fa.fai",
"cytobandURL": "https://hgdownload.soe.ucsc.edu/goldenPath/rn7/database/cytoBandIdeo.txt.gz",
"aliasURL": "https://s3.amazonaws.com/igv.org.genomes/rn7/chrAlias.tab.gz",
"aliasURL": "https://hgdownload.soe.ucsc.edu/goldenPath/rn7/bigZips/rn7.chromAlias.txt",
"twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/rn7/bigZips/rn7.2bit",
"chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/rn7/bigZips/rn7.chrom.sizes",
"chromosomeOrder": "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chrX,chrY",
"tracks": [
{
"name": "Genes",
"format": "refgene",
"url": "https://s3.amazonaws.com/igv.org.genomes/rn7/ncbiRefSeq.txt.gz",
"indexURL": "https://s3.amazonaws.com/igv.org.genomes/rn7/ncbiRefSeq.txt.gz.tbi",
"order": 1000000,
"visibilityWindow": -1,
"supportsWholeGenome": false
},
{
"name": "Genes",
"format": "bed",
"url": "https://s3.amazonaws.com/igv.org.genomes/locations/geneLocations_rn7.bed.gz",
"hidden": true,
"searchable": true
"url": "https://hgdownload.soe.ucsc.edu/goldenPath/rn7/database/ncbiRefSeq.txt.gz",
"order": 1000000
}
]
},
Expand Down Expand Up @@ -274,23 +267,15 @@
"fastaURL": "https://s3.amazonaws.com/igv.org.genomes/gorGor6/gorGor6.fa",
"indexURL": "https://s3.amazonaws.com/igv.org.genomes/gorGor6/gorGor6.fa.fai",
"cytobandURL": "https://hgdownload.soe.ucsc.edu/goldenPath/gorGor6/database/cytoBandIdeo.txt.gz",
"aliasURL": "https://s3.amazonaws.com/igv.org.genomes/gorGor6/chrAlias.tab.gz",
"aliasURL": "https://hgdownload.soe.ucsc.edu/goldenPath/gorGor6/bigZips/gorGor6.chromAlias.txt",
"twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/gorGor6/bigZips/gorGor6.2bit",
"chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/gorGor6/bigZips/gorGor6.chrom.sizes",
"tracks": [
{
"name": "Refseq Genes",
"format": "refgene",
"url": "https://s3.amazonaws.com/igv.org.genomes/gorGor6/ncbiRefSeq.txt.gz",
"indexURL": "https://s3.amazonaws.com/igv.org.genomes/gorGor6/ncbiRefSeq.txt.gz.tbi",
"order": 1000000,
"visibilityWindow": -1,
"supportsWholeGenome": false
},
{
"name": "Genes",
"format": "bed",
"url": "https://s3.amazonaws.com/igv.org.genomes/locations/geneLocations_gorGor6.bed.gz",
"hidden": true,
"searchable": true
"url": "https://hgdownload.soe.ucsc.edu/goldenPath/gorGor6/database/ncbiRefSeq.txt.gz",
"order": 1000000
}
],
"chromosomeOrder": "chr1,chr2A,chr2B,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX"
Expand Down Expand Up @@ -320,23 +305,17 @@
"fastaURL": "https://s3.amazonaws.com/igv.org.genomes/panTro6/panTro6.fa",
"indexURL": "https://s3.amazonaws.com/igv.org.genomes/panTro6/panTro6.fa.fai",
"cytobandURL": "https://hgdownload.soe.ucsc.edu/goldenPath/panTro6/database/cytoBandIdeo.txt.gz",
"twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/panTro6/bigZips/panTro6.2bit",
"chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/panTro6/bigZips/panTro6.chrom.sizes",
"chromAliasBbURL": "https://hgdownload.soe.ucsc.edu/goldenPath/panTro6/bigZips/panTro6.chromAlias.bb",
"nameSet": "ucsc",
"chromosomeOrder": "chr1,chr2A,chr2B,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY",
"tracks": [
{
"name": "Refseq Genes",
"format": "refgene",
"url": "https://s3.amazonaws.com/igv.org.genomes/panTro6/ncbiRefSeq.txt.gz",
"indexURL": "https://s3.amazonaws.com/igv.org.genomes/panTro6/ncbiRefSeq.txt.gz.tbi",
"order": 1000000,
"visibilityWindow": -1,
"supportsWholeGenome": false
},
{
"name": "Genes",
"format": "bed",
"url": "https://s3.amazonaws.com/igv.org.genomes/locations/geneLocations_panTro6.bed.gz",
"hidden": true,
"searchable": true
"url": "https://hgdownload.soe.ucsc.edu/goldenPath/panTro6/database/ncbiRefSeq.txt.gz",
"order": 1000000
}
]
},
Expand Down Expand Up @@ -398,23 +377,15 @@
"fastaURL": "https://s3.amazonaws.com/igv.org.genomes/macFas5/macFas5.fa",
"indexURL": "https://s3.amazonaws.com/igv.org.genomes/macFas5/macFas5.fa.fai",
"cytobandURL": "https://hgdownload.soe.ucsc.edu/goldenPath/macFas5/database/cytoBandIdeo.txt.gz",
"aliasURL": "https://s3.amazonaws.com/igv.org.genomes/macFas5/chrAlias.tab.gz",
"aliasURL": "https://hgdownload.soe.ucsc.edu/goldenPath/macFas5/bigZips/macFas5.chromAlias.txt",
"twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/macFas5/bigZips/macFas5.2bit",
"chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/macFas5/bigZips/macFas5.chrom.sizes",
"tracks": [
{
"name": "Genes",
"format": "refgene",
"url": "https://s3.amazonaws.com/igv.org.genomes/macFas5/ncbiRefSeq.txt.gz",
"indexURL": "https://s3.amazonaws.com/igv.org.genomes/macFas5/ncbiRefSeq.txt.gz.tbi",
"visibilityWindow": -1,
"supportsWholeGenome": false,
"url": "https://hgdownload.soe.ucsc.edu/goldenPath/macFas5/database/ncbiRefSeq.txt.gz",
"order": 1000000
},
{
"name": "Genes",
"format": "bed",
"url": "https://s3.amazonaws.com/igv.org.genomes/locations/geneLocations_macFas5.bed.gz",
"hidden": true,
"searchable": true
}
]
},
Expand Down Expand Up @@ -473,28 +444,40 @@
]
},
{
"id": "canFam3",
"name": "Dog (Broad CanFam3.1/canFam3)",
"fastaURL": "https://s3.amazonaws.com/igv.org.genomes/canFam3/canFam3.fa",
"indexURL": "https://s3.amazonaws.com/igv.org.genomes/canFam3/canFam3.fa.fai",
"cytobandURL": "https://s3.amazonaws.com/igv.org.genomes/canFam3/cytoBandIdeo.txt.gz",
"id": "canFam6",
"name": "Dog (canFam6) ",
"cytobandURL": "https://hgdownload.soe.ucsc.edu/goldenPath/canFam6/database/cytoBandIdeo.txt.gz",
"twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/canFam6/bigZips/canFam6.2bit",
"chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/canFam6/bigZips/canFam6.chrom.sizes",
"aliasURL": "https://hgdownload.soe.ucsc.edu/goldenPath/canFam6/bigZips/canFam6.chromAlias.txt",
"nameSet": "ucsc",
"chromosomeOrder": "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chr23,chr24,chr25,chr26,chr27,chr28,chr29,chr30,chr31,chr32,chr33,chr34,chr35,chr36,chr37,chr38,chrX",
"tracks": [
{
"name": "Refseq Genes",
"name": "Genes",
"format": "refgene",
"url": "https://s3.amazonaws.com/igv.org.genomes/canFam3/ncbiRefSeq.sorted.txt.gz",
"indexURL": "https://s3.amazonaws.com/igv.org.genomes/canFam3/ncbiRefSeq.sorted.txt.gz.tbi",
"indexed": false,
"order": 1000000,
"visibilityWindow": -1,
"supportsWholeGenome": false
},
"url": "https://hgdownload.soe.ucsc.edu/goldenPath/canFam6/database/ncbiRefSeq.txt.gz",
"order": 1000000
}
]
},
{
"id": "canFam5",
"name": "Dog (canFam5) ",
"fastaURL": "https://s3.amazonaws.com/igv.org.genomes/canFam5/canFam5.fa",
"indexURL": "https://s3.amazonaws.com/igv.org.genomes/canFam5/canFam5.fa.fai",
"cytobandURL": "https://hgdownload.soe.ucsc.edu/goldenPath/canFam5/database/cytoBandIdeo.txt.gz",
"twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/canFam5/bigZips/canFam5.2bit",
"chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/canFam5/bigZips/canFam5.chrom.sizes",
"chromAliasBbURL": "https://hgdownload.soe.ucsc.edu/goldenPath/canFam5/bigZips/canFam5.chromAlias.bb",
"nameSet": "ucsc",
"chromosomeOrder": "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chr23,chr24,chr25,chr26,chr27,chr28,chr29,chr30,chr31,chr32,chr33,chr34,chr35,chr36,chr37,chr38,chrX",
"tracks": [
{
"name": "Genes",
"format": "bed",
"url": "https://s3.amazonaws.com/igv.org.genomes/locations/geneLocations_canFam3.bed.gz",
"hidden": true,
"searchable": true
"format": "refgene",
"url": "https://hgdownload.soe.ucsc.edu/goldenPath/canFam5/database/refGene.txt.gz",
"order": 1000000
}
]
},
Expand All @@ -516,26 +499,26 @@
]
},
{
"id": "canFam5",
"name": "Dog (canFam5) ",
"fastaURL": "https://s3.amazonaws.com/igv.org.genomes/canFam5/canFam5.fa",
"indexURL": "https://s3.amazonaws.com/igv.org.genomes/canFam5/canFam5.fa.fai",
"cytobandURL": "https://hgdownload.soe.ucsc.edu/goldenPath/canFam5/database/cytoBandIdeo.txt.gz",
"aliasURL": "https://s3.amazonaws.com/igv.org.genomes/canFam5/chrAlias.tab.gz",
"id": "canFam3",
"name": "Dog (Broad CanFam3.1/canFam3)",
"fastaURL": "https://s3.amazonaws.com/igv.org.genomes/canFam3/canFam3.fa",
"indexURL": "https://s3.amazonaws.com/igv.org.genomes/canFam3/canFam3.fa.fai",
"cytobandURL": "https://s3.amazonaws.com/igv.org.genomes/canFam3/cytoBandIdeo.txt.gz",
"tracks": [
{
"name": "Genes",
"name": "Refseq Genes",
"format": "refgene",
"url": "https://s3.amazonaws.com/igv.org.genomes/canFam5/refGene.txt.gz",
"indexURL": "https://s3.amazonaws.com/igv.org.genomes/canFam5/refGene.txt.gz.tbi",
"url": "https://s3.amazonaws.com/igv.org.genomes/canFam3/ncbiRefSeq.sorted.txt.gz",
"indexURL": "https://s3.amazonaws.com/igv.org.genomes/canFam3/ncbiRefSeq.sorted.txt.gz.tbi",
"indexed": false,
"order": 1000000,
"visibilityWindow": -1,
"supportsWholeGenome": false
},
{
"name": "Genes",
"format": "bed",
"url": "https://s3.amazonaws.com/igv.org.genomes/locations/geneLocations_canFam5.bed.gz",
"url": "https://s3.amazonaws.com/igv.org.genomes/locations/geneLocations_canFam3.bed.gz",
"hidden": true,
"searchable": true
}
Expand All @@ -546,23 +529,16 @@
"name": "Cow (ARS-UCD1.2/bosTau9)",
"fastaURL": "https://s3.amazonaws.com/igv.org.genomes/bosTau9/bosTau9.fa",
"indexURL": "https://s3.amazonaws.com/igv.org.genomes/bosTau9/bosTau9.fa.fai",
"cytobandURL": "https://s3.amazonaws.com/igv.org.genomes/bosTau9/cytoBandIdeo.txt.gz",
"cytobandURL": "https://hgdownload.soe.ucsc.edu/goldenPath/bosTau9/database/cytoBandIdeo.txt.gz",
"twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/bosTau9/bigZips/bosTau9.2bit",
"chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/bosTau9/bigZips/bosTau9.chrom.sizes",
"aliasURL": "https://hgdownload.soe.ucsc.edu/goldenPath/bosTau9/bigZips/bosTau9.chromAlias.txt",
"tracks": [
{
"name": "Refseq Genes",
"format": "refgene",
"url": "https://s3.amazonaws.com/igv.org.genomes/bosTau9/ncbiRefSeq.sorted.txt.gz",
"indexURL": "https://s3.amazonaws.com/igv.org.genomes/bosTau9/ncbiRefSeq.sorted.txt.gz.tbi",
"order": 1000000,
"visibilityWindow": -1,
"supportsWholeGenome": false
},
{
"name": "Genes",
"format": "bed",
"url": "https://s3.amazonaws.com/igv.org.genomes/locations/geneLocations_bosTau9.bed.gz",
"hidden": true,
"searchable": true
"url": "https://hgdownload.soe.ucsc.edu/goldenPath/bosTau9/database/ncbiRefSeq.txt.gz",
"order": 1000000
}
]
},
Expand Down Expand Up @@ -622,15 +598,16 @@
"name": " Chicken (galGal6)",
"fastaURL": "https://s3.amazonaws.com/igv.org.genomes/galGal6/galGal6.fa",
"indexURL": "https://s3.amazonaws.com/igv.org.genomes/galGal6/galGal6.fa.fai",
"cytobandURL": "https://s3.amazonaws.com/igv.org.genomes/galGal6/cytoBandIdeo.txt",
"cytobandURL": "https://hgdownload.soe.ucsc.edu/goldenPath/galGal6/database/cytoBandIdeo.txt.gz",
"twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/galGal6/bigZips/galGal6.2bit",
"chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/galGal6/bigZips/galGal6.chrom.sizes",
"aliasURL": "https://hgdownload.soe.ucsc.edu/goldenPath/galGal6/bigZips/galGal6.chromAlias.txt",
"tracks": [
{
"name": "NCBI Refseq Genes",
"format": "refgene",
"url": "https://s3.amazonaws.com/igv.org.genomes/galGal6/ncbiRefSeq.txt.gz",
"indexURL": "https://s3.amazonaws.com/igv.org.genomes/galGal6/ncbiRefSeq.txt.gz.tbi",
"order": 1000000,
"searchable": true
"url": "https://hgdownload.soe.ucsc.edu/goldenPath/galGal6/database/ncbiRefSeq.txt.gz",
"order": 1000000
}
]
},
Expand Down Expand Up @@ -851,7 +828,11 @@
"name": "A. thaliana (TAIR 10)",
"fastaURL": "https://s3.amazonaws.com/igv.org.genomes/tair10/TAIR10_chr_all.fas",
"indexURL": "https://s3.amazonaws.com/igv.org.genomes/tair10/TAIR10_chr_all.fas.fai",
"aliasURL": "https://s3.amazonaws.com/igv.org.genomes/tair10/TAIR10_alias.tab",
"twoBitURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/001/735/GCF_000001735.3/GCF_000001735.3.2bit",
"chromSizesURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/001/735/GCF_000001735.3/GCF_000001735.3.chrom.sizes.txt",
"aliasURL": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/001/735/GCF_000001735.3/GCF_000001735.3.chromAlias.txt",
"nameSet": "ucsc",
"chromosomeOrder": "NC_003070.9,NC_003071.7,NC_003074.8,NC_003075.7,NC_003076.8",
"tracks": [
{
"name": "Genes",
Expand Down Expand Up @@ -944,4 +925,4 @@
}
]
}
]
]

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