{
    "content_blobs": [],
    "create_time": "2024-11-04",
    "creators": [
        "Diego De Panis",
        "ERGA"
    ],
    "description": "**Assembly Evaluation for ERGA-BGE Reports**\r\n\r\n_One Assembly, HiFi WGS reads + HiC reads_\r\n\r\nThe workflow requires the following:\r\n* Species Taxonomy ID number\r\n* NCBI Genome assembly accession code\r\n* BUSCO Lineage\r\n* WGS accurate reads accession code\r\n* NCBI HiC reads accession code\r\n\r\nThe workflow will get the data and process it to generate genome profiling (genomescope, smudgeplot -optional-), assembly stats (gfastats), merqury stats (QV, completeness), BUSCO, snailplot, contamination blobplot, and HiC heatmap.\r\n\r\n**Use this workflow for HiFi- or ONT-based assemblies**",
    "discussion_links": [
        {
            "id": "1133",
            "label": "",
            "url": "https://github.com/ERGA-consortium/pipelines/discussions"
        }
    ],
    "doi": "",
    "edam_operation": [
        "Genome assembly"
    ],
    "edam_topic": [
        "Genomics"
    ],
    "id": "1104",
    "latest_version": "2",
    "license": "MIT",
    "link": "https://workflowhub.eu/workflows/1104?version=2",
    "mapped_tools": [
        "bedtools",
        "blobtoolkit",
        "busco",
        "diamond",
        "genomescope_2.0",
        "gfastats",
        "hicexplorer",
        "merqury",
        "meryl",
        "minimap2",
        "ncbi_datasets",
        "rseqc",
        "smudgeplots",
        "sra-tools"
    ],
    "name": "Galaxy Workflow ERGA-BGE Genome Report ASM analyses (one-asm Long Reads + HiC)",
    "number_of_steps": 48,
    "projects": [],
    "source": "WorkflowHub",
    "tags": [
        "genome assembly",
        "genomics",
        "qc"
    ],
    "tools": [
        "__extract_dataset__",
        "__flatten__",
        "__unzip_collection__",
        "__zip_collection__",
        "bedtools",
        "bedtools_makewindowsbed",
        "bg_diamond",
        "blobtoolkit",
        "busco",
        "chromap",
        "collapse_dataset",
        "converter_fasta_to_fai",
        "cooler_cload_tabix",
        "cooler_csort_tabix",
        "cut1",
        "datasets_download_genome",
        "diamond",
        "fasterq_dump",
        "genomescope",
        "genomescope 2.0",
        "genomescope_2.0",
        "gfastats",
        "hicexplorer",
        "hicexplorer_hicmergematrixbins",
        "hicexplorer_hicplotmatrix",
        "lftp",
        "merqury",
        "meryl",
        "minimap2",
        "ncbi datasets",
        "ncbi_datasets",
        "pick_value",
        "rseqc",
        "sambamba_flagstat",
        "sambamba_merge",
        "smudgeplot",
        "smudgeplots",
        "sra software toolkit",
        "sra-tools",
        "tp_text_file_with_recurring_lines"
    ],
    "update_time": "2026-06-15",
    "versions": "2",
    "workflow_class": "Galaxy"
}