diff --git a/resources/genomes.json b/resources/genomes.json index 72c75db..fc628cb 100644 --- a/resources/genomes.json +++ b/resources/genomes.json @@ -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", @@ -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", @@ -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", @@ -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 } ] }, @@ -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" @@ -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 } ] }, @@ -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 } ] }, @@ -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 } ] }, @@ -516,18 +499,18 @@ ] }, { - "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 @@ -535,7 +518,7 @@ { "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 } @@ -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 } ] }, @@ -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 } ] }, @@ -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", @@ -944,4 +925,4 @@ } ] } -] +] \ No newline at end of file