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  "Title": "Build Custom Reference Genome for Single-Cell Multiome ATAC and\nGene Expression Data of Large-Genome Species",
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  "Description": "Provides utilities that enable researchers to build custom\nreferences for the Multiome ATAC Gene Expression sequencing\ndata for large-genome species without manual intervention.",
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        "2. {scShardSplitRef} Guided Walkthrough Using a Toy Example",
        "Installation",
        "Prerequisites",
        "Input Files",
        "Workflow",
        "1. Determine Split Regions",
        "The Help Page for determine_split_regions()",
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        "No Overlap with Gene Coordinates",
        "Overlap with Gene Coordinates",
        "2. Process a GTF file by assigning split-region sequence names",
        "The Help Page for process_gtf()",
        "Usage Example: process_gtf()",
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        "Installation",
        "Prerequisites",
        "Input Files",
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        "Step-1",
        "The Help Page for the determine_split_regions() Function",
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        "Step-2",
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        "Generate Gene Annotation (GTF) File in Compatible to Cell Ranger ARC Format",
        "Step-3",
        "Step-4",
        "Prepare config File",
        "Run Cell Ranger ARC",
        "Citation",
        "License",
        "Contributing",
        "Acknowledgements"
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      "modified": "2026-07-23 12:30:02",
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