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react-msaview JBrowse combined-view demo config (temp for testing)
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| { | |
| "plugins": [ | |
| { | |
| "name": "MsaView", | |
| "url": "https://jbrowse.org/plugins/jbrowse-plugin-msaview/dist/jbrowse-plugin-msaview.umd.production.min.js" | |
| } | |
| ], | |
| "assemblies": [ | |
| { | |
| "name": "hg38", | |
| "aliases": [ | |
| "GRCh38" | |
| ], | |
| "sequence": { | |
| "type": "ReferenceSequenceTrack", | |
| "trackId": "P6R5xbRqRr", | |
| "adapter": { | |
| "type": "BgzipFastaAdapter", | |
| "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz" | |
| } | |
| }, | |
| "refNameAliases": { | |
| "adapter": { | |
| "type": "RefNameAliasAdapter", | |
| "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/hg38_aliases.txt" | |
| } | |
| }, | |
| "cytobands": { | |
| "adapter": { | |
| "type": "CytobandAdapter", | |
| "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/cytoBand.txt" | |
| } | |
| } | |
| } | |
| ], | |
| "tracks": [ | |
| { | |
| "type": "FeatureTrack", | |
| "trackId": "hg38-ncbiRefSeq", | |
| "name": "NCBI RefSeq genes", | |
| "assemblyNames": [ | |
| "hg38" | |
| ], | |
| "category": [ | |
| "Genes" | |
| ], | |
| "adapter": { | |
| "type": "Gff3TabixAdapter", | |
| "gffGzLocation": { | |
| "uri": "https://jbrowse.org/ucsc/hg38/ncbiRefSeq.gff.gz" | |
| }, | |
| "index": { | |
| "indexType": "CSI", | |
| "location": { | |
| "uri": "https://jbrowse.org/ucsc/hg38/ncbiRefSeq.gff.gz.csi" | |
| } | |
| } | |
| } | |
| }, | |
| { | |
| "type": "MafTrack", | |
| "trackId": "hg38-multiz470way", | |
| "name": "Multiz 470-way mammal alignment", | |
| "assemblyNames": [ | |
| "hg38" | |
| ], | |
| "category": [ | |
| "Comparative genomics" | |
| ], | |
| "adapter": { | |
| "type": "BigMafAdapter", | |
| "bigBedLocation": { | |
| "uri": "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/multiz470way/multiz470way.bigMaf" | |
| }, | |
| "samples": [ | |
| { | |
| "id": "hg38", | |
| "label": "human" | |
| }, | |
| { | |
| "id": "HLnomLeu4", | |
| "label": "gibbon" | |
| }, | |
| { | |
| "id": "HLpapAnu5", | |
| "label": "olive baboon" | |
| }, | |
| { | |
| "id": "HLmacFas6", | |
| "label": "macaque" | |
| }, | |
| { | |
| "id": "HLcalJac4", | |
| "label": "marmoset" | |
| }, | |
| { | |
| "id": "HLratNor7", | |
| "label": "rat" | |
| }, | |
| { | |
| "id": "HLoryCunCun4", | |
| "label": "rabbit" | |
| }, | |
| { | |
| "id": "HLsciVul1", | |
| "label": "red squirrel" | |
| }, | |
| { | |
| "id": "HLmusFur2", | |
| "label": "ferret" | |
| }, | |
| { | |
| "id": "HLailMel2", | |
| "label": "giant panda" | |
| }, | |
| { | |
| "id": "HLmyoLuc1", | |
| "label": "little brown bat" | |
| }, | |
| { | |
| "id": "HLturTru4", | |
| "label": "bottlenose dolphin" | |
| }, | |
| { | |
| "id": "HLbalMus1", | |
| "label": "blue whale" | |
| }, | |
| { | |
| "id": "HLbosInd2", | |
| "label": "zebu cattle" | |
| }, | |
| { | |
| "id": "HLchoHof3", | |
| "label": "sloth" | |
| }, | |
| { | |
| "id": "HLtolMat1", | |
| "label": "armadillo" | |
| }, | |
| { | |
| "id": "HLproCap3", | |
| "label": "rock hyrax" | |
| }, | |
| { | |
| "id": "HLdidVir1", | |
| "label": "opossum" | |
| }, | |
| { | |
| "id": "HLmacGig1", | |
| "label": "gray kangaroo" | |
| } | |
| ], | |
| "nhLocation": { | |
| "uri": "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/multiz470way/hg38.470way.nh" | |
| } | |
| } | |
| } | |
| ] | |
| } |
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| { | |
| "plugins": [ | |
| { | |
| "name": "MsaView", | |
| "url": "https://jbrowse.org/plugins/jbrowse-plugin-msaview/dist/jbrowse-plugin-msaview.umd.production.min.js" | |
| } | |
| ], | |
| "assemblies": [ | |
| { | |
| "name": "hg38", | |
| "aliases": ["GRCh38"], | |
| "sequence": { | |
| "type": "ReferenceSequenceTrack", | |
| "trackId": "P6R5xbRqRr", | |
| "adapter": { | |
| "type": "BgzipFastaAdapter", | |
| "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz" | |
| } | |
| }, | |
| "refNameAliases": { | |
| "adapter": { | |
| "type": "RefNameAliasAdapter", | |
| "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/hg38_aliases.txt" | |
| } | |
| }, | |
| "cytobands": { | |
| "adapter": { | |
| "type": "CytobandAdapter", | |
| "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/cytoBand.txt" | |
| } | |
| } | |
| } | |
| ], | |
| "tracks": [ | |
| { | |
| "type": "FeatureTrack", | |
| "trackId": "hg38-ncbiRefSeq", | |
| "name": "NCBI RefSeq genes", | |
| "assemblyNames": ["hg38"], | |
| "category": ["Genes"], | |
| "adapter": { | |
| "type": "Gff3TabixAdapter", | |
| "gffGzLocation": { | |
| "uri": "https://jbrowse.org/ucsc/hg38/ncbiRefSeq.gff.gz" | |
| }, | |
| "index": { | |
| "indexType": "CSI", | |
| "location": { | |
| "uri": "https://jbrowse.org/ucsc/hg38/ncbiRefSeq.gff.gz.csi" | |
| } | |
| } | |
| } | |
| }, | |
| { | |
| "type": "MafTrack", | |
| "trackId": "hg38-multiz470way", | |
| "name": "Multiz 470-way mammal alignment", | |
| "assemblyNames": ["hg38"], | |
| "category": ["Comparative genomics"], | |
| "adapter": { | |
| "type": "BigMafAdapter", | |
| "bigBedLocation": { | |
| "uri": "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/multiz470way/multiz470way.bigMaf" | |
| }, | |
| "samples": [ | |
| { "id": "hg38", "label": "human" }, | |
| { "id": "HLnomLeu4", "label": "gibbon" }, | |
| { "id": "HLpapAnu5", "label": "olive baboon" }, | |
| { "id": "HLmacFas6", "label": "macaque" }, | |
| { "id": "HLcalJac4", "label": "marmoset" }, | |
| { "id": "HLratNor7", "label": "rat" }, | |
| { "id": "HLoryCunCun4", "label": "rabbit" }, | |
| { "id": "HLsciVul1", "label": "red squirrel" }, | |
| { "id": "HLmusFur2", "label": "ferret" }, | |
| { "id": "HLailMel2", "label": "giant panda" }, | |
| { "id": "HLmyoLuc1", "label": "little brown bat" }, | |
| { "id": "HLturTru4", "label": "bottlenose dolphin" }, | |
| { "id": "HLbalMus1", "label": "blue whale" }, | |
| { "id": "HLbosInd2", "label": "zebu cattle" }, | |
| { "id": "HLchoHof3", "label": "sloth" }, | |
| { "id": "HLtolMat1", "label": "armadillo" }, | |
| { "id": "HLproCap3", "label": "rock hyrax" }, | |
| { "id": "HLdidVir1", "label": "opossum" }, | |
| { "id": "HLmacGig1", "label": "gray kangaroo" } | |
| ] | |
| } | |
| } | |
| ] | |
| } |
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