{
    "content_blobs": [],
    "create_time": "2025-06-19",
    "creators": [
        "Fabrice Touzain",
        "This study was founded by the French National Research Agency and by Sant\u00e9 publique France as part of the project \"EMERGEN\". Anses Ploufragan research was also supported by Agglom\u00e9ration de Saint-Brieuc, D\u00e9partement des C\u00f4tes d'Armor and R\u00e9gion Bretagne"
    ],
    "description": "Using:\r\n- vadr annotation (**model to select**)\r\n- vardict variant caller\r\n- coverage depth\r\n\r\nProvides summarizing files:\r\n- **png image** of **variant calling** with **annotations** and **coverage depths**\r\n- **tsv file** with all information of **significant variants only**\r\n- **vcf file** with all information of **significant variants only** (to allow downstream NextStrain analyses)\r\n",
    "discussion_links": [],
    "doi": "",
    "edam_operation": [],
    "edam_topic": [],
    "id": "1741",
    "latest_version": "1",
    "license": "GPL-3.0-or-later",
    "link": "https://workflowhub.eu/workflows/1741?version=1",
    "mapped_tools": [
        "bcftools",
        "fastp",
        "fastx-toolkit",
        "minimap2",
        "samtools",
        "vardict"
    ],
    "name": "vvv2_align_SE_minimap2_pacbio",
    "number_of_steps": 12,
    "projects": [],
    "source": "WorkflowHub",
    "tags": [
        "virus",
        "bbmap",
        "display",
        "pacbio",
        "vadr",
        "vardict",
        "variant_calling",
        "vvv2_display"
    ],
    "tools": [
        "bcftools",
        "bcftools_call",
        "bcftools_consensus",
        "bcftools_mpileup",
        "cshl_fasta_formatter",
        "fastp",
        "fastx-toolkit",
        "minimap2",
        "samtools",
        "samtools_depth",
        "samtools_rmdup",
        "vadr",
        "vardict",
        "vardict_java",
        "vvv2_display"
    ],
    "update_time": "2026-05-13",
    "versions": "1",
    "workflow_class": "Galaxy"
}