[
    {
        "id": "flye",
        "name": "flye",
        "article": "s41592-020-00971-x",
        "website": "https:\/\/github.com\/fenderglass\/Flye\/blob\/flye\/docs\/FAQ.md",
        "git": "https:\/\/github.com\/fenderglass\/Flye",
        "description": "Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies.",
        "version": "2.9.2",
        "documentation": "https:\/\/github.com\/fenderglass\/Flye\/tree\/flye\/docs",
        "multiqc": "custom",
        "commands": [
            {
                "name": "flye",
                "cname": "Flye assembler",
                "command": "flye",
                "category": "assembly",
                "output_dir": "flye",
                "inputs": [
                    {
                        "name": "read",
                        "type": "reads"
                    }
                ],
                "outputs": [
                    {
                        "name": "assembly_info",
                        "type": "tsv",
                        "file": "assembly_info.txt",
                        "description": "Extra information about contigs"
                    },
                    {
                        "name": "assembly_fasta",
                        "type": "contigs",
                        "file": "assembly.fasta",
                        "description": "Final assembly. Contains contigs and possibly scaffolds in fasta format"
                    }
                ],
                "options": [
                    {
                        "name": "flye_threads",
                        "prefix": "-t",
                        "type": "numeric",
                        "value": 4,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Number of threads to use"
                    },
                    {
                        "name": "flye_pacbio_oxfordNanopore",
                        "type": "select",
                        "value": "--nano-hq",
                        "choices": [
                            {
                                "Pacbio raw": "--pacbio-raw"
                            },
                            {
                                "Pacbio corre": "--pacbio-corr"
                            },
                            {
                                "Pacbio hifi": "--pacbio-hifi"
                            },
                            {
                                "ONT raw": "--nano-raw"
                            },
                            {
                                "ONT corr": "--nano-corr"
                            },
                            {
                                "ONT hq": "--nano-hq"
                            }
                        ],
                        "label": "Reads type"
                    },
                    {
                        "name": "flye_keep_haplotypes",
                        "prefix": "--keep-haplotypes",
                        "type": "checkbox",
                        "value": false,
                        "label": "do not collapse alternative haplotypes"
                    },
                    {
                        "name": "flye_scaffold",
                        "prefix": "--scaffold",
                        "type": "checkbox",
                        "value": false,
                        "label": "enable scaffolding using graph"
                    }
                ]
            }
        ],
        "install": [],
        "citations": {
            "minimap2": [
                "Mikhail Kolmogorov, Derek M. Bickhart, Bahar Behsaz, Alexey Gurevich, Mikhail Rayko, Sung Bong Shin, Kristen Kuhn, Jeffrey Yuan, Evgeny Polevikov, Timothy P. L. Smith and Pavel A. Pevzner metaFlye: scalable long-read metagenome assembly using repeat graphs",
                "Nature Methods",
                "2020\""
            ]
        },
        "yaml": "{\n  id: flye,\n  name: flye,\n  article: \"s41592-020-00971-x\",\n  website: \"https:\/\/github.com\/fenderglass\/Flye\/blob\/flye\/docs\/FAQ.md\",\n  git: \"https:\/\/github.com\/fenderglass\/Flye\",\n  description: \"Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies.\",\n  version: \"2.9.2\",\n  documentation: \"https:\/\/github.com\/fenderglass\/Flye\/tree\/flye\/docs\",\n  multiqc: \"custom\",\n  commands:\n    [\n      {\n        name: flye,\n        cname: \"Flye assembler\",\n        command:  flye,\n        category: \"assembly\",\n        output_dir: flye,\n        inputs: [{ name: read, type: \"reads\" }],\n        outputs:\n        [\n          { name: assembly_info, type: \"tsv\", file: assembly_info.txt , description: \"Extra information about contigs\" },\n          { name: assembly_fasta, type: \"contigs\", file: assembly.fasta, description: \"Final assembly. Contains contigs and possibly scaffolds in fasta format\" }\n        ],\n        options:\n          [\n            {\n              name: flye_threads,\n              prefix: -t,\n              type: numeric,\n              value: 4,\n              min: 1,\n              max: NA,\n              step: 1,\n              label: \"Number of threads to use\",\n            },\n            {\n              name: \"flye_pacbio_oxfordNanopore\",\n              type: \"select\",\n              value: \"--nano-hq\",\n              choices: [\n                Pacbio raw: --pacbio-raw,\n                Pacbio corre: --pacbio-corr,\n                Pacbio hifi: --pacbio-hifi,\n                ONT raw: --nano-raw,\n                ONT corr: --nano-corr,\n                ONT hq: '--nano-hq'\n                ],\n              label: \"Reads type\",\n            },\n            {\n            name: flye_keep_haplotypes,\n            prefix: \"--keep-haplotypes\",\n            type: checkbox,\n            value: False,\n            label: \"do not collapse alternative haplotypes\",\n            },\n            {\n            name: flye_scaffold,\n            prefix: \"--scaffold\",\n            type: checkbox,\n            value: False,\n            label: \"enable scaffolding using graph\",\n            },\n          ],\n      },\n    ],\n  install: {\n    # flye: [\n    #   \"cd \/opt\/biotools\",\n    #   \"git clone https:\/\/github.com\/fenderglass\/Flye\",\n    #   \"cd Flye\",\n    #   \"python setup.py install\",\n    #   \"ENV PATH $PATH:\/opt\/biotools\/conda\/bin\/ \"\n    # ]\n  },\n  citations:  {\n    minimap2: [\n      \"Mikhail Kolmogorov, Derek M. Bickhart, Bahar Behsaz, Alexey Gurevich, Mikhail Rayko, Sung Bong Shin, Kristen Kuhn, Jeffrey Yuan, Evgeny Polevikov, Timothy P. L. Smith and Pavel A. Pevzner metaFlye: scalable long-read metagenome assembly using repeat graphs\", Nature Methods, 2020\"\n    ]\n  }\n}"
    }
]