[
    {
        "id": "miniasm",
        "name": "miniasm",
        "article": "10.1093\/bioinformatics\/btw152",
        "website": "https:\/\/github.com\/lh3\/miniasm",
        "git": "https:\/\/github.com\/lh3\/miniasm",
        "description": "Ultrafast de novo assembly for long noisy reads (though having no consensus step)",
        "version": "0.3",
        "documentation": "https:\/\/github.com\/lh3\/miniasm\/blob\/master\/README.md",
        "multiqc": "custom",
        "commands": [
            {
                "name": "miniasm",
                "cname": "Miniasm",
                "command": "miniasm",
                "category": "assembly",
                "output_dir": "miniasm",
                "inputs": [
                    {
                        "name": "read",
                        "type": "reads"
                    },
                    {
                        "name": "paf",
                        "type": "paf.gz"
                    }
                ],
                "outputs": [
                    {
                        "name": "assembly_gfa",
                        "type": "gfa",
                        "file": "reads.gfa",
                        "description": "Assembly graph file"
                    },
                    {
                        "name": "assembly_fasta",
                        "type": "contigs",
                        "file": "reads.fasta",
                        "description": "Assembly fasta file"
                    }
                ],
                "options": []
            }
        ],
        "install": [],
        "citations": {
            "miniasm": [
                "Heng Li, Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences, Bioinformatics, Volume 32, Issue 14, 15 July 2016, Pages 2103-2110, https:\/\/doi.org\/10.1093\/bioinformatics\/btw152"
            ]
        },
        "yaml": "{\n  id: miniasm,\n  name: miniasm,\n  article: \"10.1093\/bioinformatics\/btw152\",\n  website: \"https:\/\/github.com\/lh3\/miniasm\",\n  git: \"https:\/\/github.com\/lh3\/miniasm\",\n  description: \"Ultrafast de novo assembly for long noisy reads (though having no consensus step)\",\n  version: \"0.3\",\n  documentation: \"https:\/\/github.com\/lh3\/miniasm\/blob\/master\/README.md\",\n  multiqc: \"custom\",\n  commands:\n    [\n      {\n        name: miniasm,\n        cname: \"Miniasm\",\n        command:  miniasm,\n        category: \"assembly\",\n        output_dir: miniasm,\n        inputs: [ \n          {name: read, type: \"reads\" },\n          {name: paf, type: \"paf.gz\" }\n        ],\n        outputs:\n        [\n          { name: assembly_gfa , type: \"gfa\", file: \"reads.gfa\" , description: \"Assembly graph file\" },\n          { name: assembly_fasta , type: \"contigs\", file: \"reads.fasta\" , description: \"Assembly fasta file\" }\n        ],\n        options:\n          [\n            \n          ],\n      },\n    ],\n  install: {\n    # miniasm: [\n    #   \"cd \/opt\/biotools\",\n    #   \"wget -O miniasm.tar.gz https:\/\/github.com\/lh3\/miniasm\/archive\/v0.3.tar.gz\",\n    #   \"tar -xvzf miniasm.tar.gz\",\n    #   \"cd miniasm-0.3\",\n    #   \"make -j 10\",\n    #   \"cd .. rm miniasm.tar.gz\",\n    #   \"ENV PATH \/opt\/biotools\/miniasm-0.3:$PATH\"\n    # ]\n  },\n  citations:  {\n    miniasm: [\n      \"Heng Li, Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences, Bioinformatics, Volume 32, Issue 14, 15 July 2016, Pages 2103-2110, https:\/\/doi.org\/10.1093\/bioinformatics\/btw152\"\n    ]\n  }\n}\n"
    }
]