genome.json

{
    "references": {
        "hg38_41": {
            "GENOME_FA":      "https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_42/GRCh38.primary_assembly.genome.fa.gz",
            "TRANSCRIPTS_FA": "https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_42/gencode.v42.transcripts.fa.gz",
            "GTF_FILE":       "https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_42/gencode.v42.primary_assembly.annotation.gtf.gz",
            "SQANTI_CAGEPEAK": "/data/OpenOmics/references/modr/sqanti3/data/ref_TSS_annotation/human.refTSS_v3.1.hg38.bed"
        },
        "mm39_M31": {
            "GENOME_FA":      "https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M31/GRCm39.primary_assembly.genome.fa.gz",
            "TRANSCRIPTS_FA": "https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M31/gencode.vM31.transcripts.fa.gz",
            "GTF_FILE":       "https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M31/gencode.vM31.primary_assembly.annotation.gtf.gz",
            "SQANTI_CAGEPEAK": "/data/OpenOmics/references/modr/sqanti3/data/ref_TSS_annotation/mouse.refTSS_v3.1.GRCm39.bed"
        },
        "mm10_M25": {
            "GENOME_FA":      "https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M25/GRCm38.primary_assembly.genome.fa.gz",
            "TRANSCRIPTS_FA": "https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M25/gencode.vM25.transcripts.fa.gz",
            "GTF_FILE":       "https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M25/gencode.vM25.primary_assembly.annotation.gtf.gz",
            "SQANTI_CAGEPEAK": "/data/OpenOmics/references/modr/sqanti3/data/ref_TSS_annotation/mouse.refTSS_v3.1.mm10.bed"
        },
        "DINOPORE_CLASSREF": "/data/OpenOmics/references/modr/truthsets/groundtruth_class_regression.tsv",
        "DINOPORE_MODELS": "/data/OpenOmics/references/modr/model",
        "DINOPORE_CODE": "/data/OpenOmics/references/modr/code",
        "SQANTI_POLYA_MOTIF_LIST": "/data/OpenOmics/references/modr/sqanti3/data/polyA_motifs/mouse_and_human.polyA_motif.txt"
    }
}