[
    {
        "id": "spades",
        "name": "SPAdes",
        "description": "SPAdes is an assembly toolkit containing various assembly pipelines. It works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads.",
        "version": "3.15.5",
        "website": "https:\/\/cab.spbu.ru\/software\/spades\/",
        "git": "https:\/\/github.com\/ablab\/spades",
        "documentation": "https:\/\/cab.spbu.ru\/files\/release3.15.2\/manual.html",
        "article": "10.1089\/cmb.2012.0021",
        "multiqc": "custom",
        "commands": [
            {
                "name": "spades_PE",
                "cname": "SPAdes PE",
                "category": "assembly",
                "command": "spades.py",
                "output_dir": "spades_PE",
                "inputs": [
                    {
                        "name": "read",
                        "type": "reads"
                    },
                    {
                        "name": "read2",
                        "type": "reads"
                    }
                ],
                "outputs": [
                    {
                        "name": "scaffolds",
                        "file": "scaffolds.fasta",
                        "type": "scaffolds",
                        "description": "Resulting scaffolds"
                    },
                    {
                        "name": "contigs",
                        "file": "contigs.fasta",
                        "type": "contigs",
                        "description": "Assembled contigs"
                    },
                    {
                        "name": "assembly_graph",
                        "file": "assembly_graph.fastg",
                        "type": "fastg",
                        "description": "Assembly graph"
                    },
                    {
                        "name": "assembly_graph_with_scaffolds",
                        "file": "assembly_graph_with_scaffolds.gfa",
                        "type": "gfa",
                        "description": "Assembly graph and scaffolds paths"
                    }
                ],
                "options": [
                    {
                        "name": "spades_threads",
                        "prefix": "-t",
                        "type": "numeric",
                        "value": 16,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Number of threads to use"
                    },
                    {
                        "name": "spades_k_min",
                        "prefix": "-kmin",
                        "value": 33,
                        "min": 21,
                        "max": 121,
                        "step": 1,
                        "label": "kmin: to generate a list of k-mer sizes to be used",
                        "type": "numeric"
                    },
                    {
                        "name": "spades_k_max",
                        "prefix": "kmax",
                        "value": 49,
                        "min": 33,
                        "max": 128,
                        "step": 1,
                        "label": "kmax: to generate a list of k-mer sizes to be used",
                        "type": "numeric"
                    },
                    {
                        "name": "spades_k_inc",
                        "prefix": "-kinc",
                        "value": 2,
                        "min": 1,
                        "max": 10,
                        "step": 1,
                        "label": "k increment: to generate a list of k-mer between kmin and kmax sizes to be used",
                        "type": "numeric"
                    },
                    {
                        "name": "spades_other_options",
                        "value": "",
                        "label": "Options to add to the command line",
                        "type": "text"
                    }
                ]
            },
            {
                "name": "spades_SE",
                "cname": "SPAdes SE",
                "command": "spades.py",
                "category": "assembly",
                "output_dir": "spades_SE",
                "inputs": [
                    {
                        "name": "read",
                        "type": "reads"
                    }
                ],
                "outputs": [
                    {
                        "name": "scaffolds",
                        "file": "scaffolds.fasta",
                        "type": "scaffolds",
                        "description": "Resulting scaffolds"
                    },
                    {
                        "name": "contigs",
                        "file": "contigs.fasta",
                        "type": "contigs",
                        "description": "Assembled contigs"
                    },
                    {
                        "name": "assembly_graph",
                        "file": "assembly_graph.fastg",
                        "type": "fastg",
                        "description": "Assembly graph"
                    },
                    {
                        "name": "assembly_graph_with_scaffolds",
                        "file": "assembly_graph_with_scaffolds.gfa",
                        "type": "gfa",
                        "description": "Assembly graph and scaffolds paths"
                    }
                ],
                "options": [
                    {
                        "name": "spades_threads",
                        "prefix": "-t",
                        "type": "numeric",
                        "value": 16,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Number of threads to use"
                    },
                    {
                        "name": "spades_k_min",
                        "prefix": "-kmin",
                        "value": 33,
                        "min": 21,
                        "max": 121,
                        "step": 1,
                        "label": "kmin: to generate a list of k-mer sizes to be used",
                        "type": "numeric"
                    },
                    {
                        "name": "spades_k_max",
                        "prefix": "kmax",
                        "value": 49,
                        "min": 33,
                        "max": 128,
                        "step": 1,
                        "label": "kmax: to generate a list of k-mer sizes to be used",
                        "type": "numeric"
                    },
                    {
                        "name": "spades_k_inc",
                        "prefix": "-kinc",
                        "value": 2,
                        "min": 1,
                        "max": 10,
                        "step": 1,
                        "label": "k increment: to generate a list of k-mer between kmin and kmax sizes to be used",
                        "type": "numeric"
                    },
                    {
                        "name": "spades_other_options",
                        "value": "",
                        "label": "Options to add to the command line",
                        "type": "text"
                    }
                ]
            }
        ],
        "install": [],
        "citations": {
            "spades": [
                "Bankevich, A., S. Nurk, D. Antipov, A. A. Gurevich, M. Dvorkin, A. S. Kulikov, V. M. Lesin, S. I. Nikolenko, S. Pham, A. D. Prjibelski, A. V. Pyshkin, A. V. Sirotkin, N. Vyahhi, G. Tesler, M. A. Alekseyev and P. A. Pevzner. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. Journal of Computational Biology 19: 455-477."
            ]
        },
        "yaml": "{\n  id: \"spades\",\n  name: \"SPAdes\",\n  description: \"SPAdes is an assembly toolkit containing various assembly pipelines. It works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads.\",\n  version: \"3.15.5\",\n  website: \"https:\/\/cab.spbu.ru\/software\/spades\/\",\n  git: \"https:\/\/github.com\/ablab\/spades\",\n  documentation: \"https:\/\/cab.spbu.ru\/files\/release3.15.2\/manual.html\",\n  article: \"10.1089\/cmb.2012.0021\",\n  multiqc: \"custom\",\n  commands:\n    [\n      {\n        name: \"spades_PE\",\n        cname: \"SPAdes PE\",\n        category: \"assembly\",\n        command: \"spades.py\",\n        output_dir: \"spades_PE\",\n        inputs:\n          [\n            { name: \"read\", type: \"reads\" },\n            { name: \"read2\", type: \"reads\" },\n          ],\n        outputs: [\n          {\n            name: \"scaffolds\",\n            file: \"scaffolds.fasta\",\n            type: \"scaffolds\",\n            description: \"Resulting scaffolds\"\n          },\n          {\n            name: \"contigs\",\n            file: \"contigs.fasta\",\n            type: \"contigs\",\n            description: \"Assembled contigs\",\n          },\n          {\n            name: \"assembly_graph\",\n            file: \"assembly_graph.fastg\",\n            type: \"fastg\",\n            description: \"Assembly graph\",\n          },\n          {\n            name: \"assembly_graph_with_scaffolds\",\n            file: \"assembly_graph_with_scaffolds.gfa\",\n            type: \"gfa\",\n            description: \"Assembly graph and scaffolds paths\",\n          },\n        ],\n        options:\n          [\n            {\n              name: spades_threads,\n              prefix: -t,\n              type: numeric,\n              value: 16,\n              min: 1,\n              max: NA,\n              step: 1,\n              label: \"Number of threads to use\",\n            },\n            {\n              name: \"spades_k_min\",\n              prefix: \"-kmin\",\n              value: 33,\n              min: 21,\n              max: 121,\n              step: 1,\n              label: \"kmin: to generate a list of k-mer sizes to be used\",\n              type: \"numeric\",\n            },\n            {\n              name: \"spades_k_max\",\n              prefix: \"kmax\",\n              value: 49,\n              min: 33,\n              max: 128,\n              step: 1,\n              label: \"kmax: to generate a list of k-mer sizes to be used\",\n              type: \"numeric\",\n            },            \n            {\n              name: \"spades_k_inc\",\n              prefix: \"-kinc\",\n              value: 2,\n              min: 1,\n              max: 10,\n              step: 1,\n              label: \"k increment: to generate a list of k-mer between kmin and kmax sizes to be used\",\n              type: \"numeric\",\n            },                        \n            {\n              name: \"spades_other_options\",\n              value: \"\",\n              label: \"Options to add to the command line\",\n              type: \"text\",\n            },\n          ]\n      },\n      {\n        name: \"spades_SE\",\n        cname: \"SPAdes SE\",\n        command: \"spades.py\",\n        category: \"assembly\",\n        output_dir: \"spades_SE\",\n        inputs:\n          [\n            { name: \"read\", type: \"reads\" },\n          ],\n        outputs: [\n          {\n            name: \"scaffolds\",\n            file: \"scaffolds.fasta\",\n            type: \"scaffolds\",\n            description: \"Resulting scaffolds\"\n          },\n          {\n            name: \"contigs\",\n            file: \"contigs.fasta\",\n            type: \"contigs\",\n            description: \"Assembled contigs\",\n          },\n          {\n            name: \"assembly_graph\",\n            file: \"assembly_graph.fastg\",\n            type: \"fastg\",\n            description: \"Assembly graph\",\n          },\n          {\n            name: \"assembly_graph_with_scaffolds\",\n            file: \"assembly_graph_with_scaffolds.gfa\",\n            type: \"gfa\",\n            description: \"Assembly graph and scaffolds paths\",\n          },\n        ],\n        options:\n          [\n            {\n              name: spades_threads,\n              prefix: -t,\n              type: numeric,\n              value: 16,\n              min: 1,\n              max: NA,\n              step: 1,\n              label: \"Number of threads to use\",\n            },\n            {\n              name: \"spades_k_min\",\n              prefix: \"-kmin\",\n              value: 33,\n              min: 21,\n              max: 121,\n              step: 1,\n              label: \"kmin: to generate a list of k-mer sizes to be used\",\n              type: \"numeric\",\n            },\n            {\n              name: \"spades_k_max\",\n              prefix: \"kmax\",\n              value: 49,\n              min: 33,\n              max: 128,\n              step: 1,\n              label: \"kmax: to generate a list of k-mer sizes to be used\",\n              type: \"numeric\",\n            },        \n            {\n              name: \"spades_k_inc\",\n              prefix: \"-kinc\",\n              value: 2,\n              min: 1,\n              max: 10,\n              step: 1,\n              label: \"k increment: to generate a list of k-mer between kmin and kmax sizes to be used\",\n              type: \"numeric\",\n            },                                        \n            {\n              name: \"spades_other_options\",\n              value: \"\",\n              label: \"Options to add to the command line\",\n              type: \"text\",\n            },\n          ],\n      },\n    ],\n  install:\n    {\n      # spades: [\n      #   \"apt-get update\",\n      #   \"apt-get install -y libboost-dev libopenmpi-dev libsparsehash-dev bsdmainutils\",\n      #   \"cd \/opt\/biotools\",\n      #   \"wget http:\/\/cab.spbu.ru\/files\/release3.15.2\/SPAdes-3.15.2-Linux.tar.gz\",\n      #   \"tar -xvzf SPAdes-3.15.2-Linux.tar.gz\",\n      #   \"rm SPAdes-3.15.2-Linux.tar.gz\",\n      #   \"ENV PATH \/opt\/biotools\/SPAdes-3.15.2-Linux\/bin:$PATH\"\n      # ],\n    },\n  citations:\n    {\n      spades: [\n        \"Bankevich, A., S. Nurk, D. Antipov, A. A. Gurevich, M. Dvorkin, A. S. Kulikov, V. M. Lesin, S. I. Nikolenko, S. Pham, A. D. Prjibelski, A. V. Pyshkin, A. V. Sirotkin, N. Vyahhi, G. Tesler, M. A. Alekseyev and P. A. Pevzner. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. Journal of Computational Biology 19: 455-477.\",\n      ],\n    },\n}\n"
    }
]