[ { "id": "mitoz_assemble", "name": "MitoZ assemble and find mitogenome", "article": "10.1093\/nar\/gkz173", "website": "https:\/\/github.com\/linzhi2013\/MitoZ", "git": "https:\/\/github.com\/linzhi2013\/MitoZ", "description": "A toolkit for assembly, annotation, and visualization of animal mitochondrial genomes", "version": "3.5", "documentation": "https:\/\/github.com\/linzhi2013\/MitoZ", "multiqc": "custom", "commands": [ { "name": "mitoz_assemble_SE", "cname": "MitoZ Assemble SE", "command": "mitoz assemble ", "category": "assembly", "output_dir": "mitoz_assemble_SE", "inputs": [ { "name": "read", "type": "reads" } ], "outputs": [ { "name": "read_assembled", "type": "contigs", "file": "final.contigs.fa", "description": "Reads assembled" }, { "name": "mitogenome", "type": "contigs", "file": "{assembler}.mitogenome.fa", "description": "mitochondrial sequences found" } ], "options": [ { "name": "mitoz_assemble_assembler", "type": "radio", "value": "megahit", "choices": [ { "megahit": "megahit" }, { "spades": "spades" }, { "mitoassemble": "mitoassemble" } ], "label": "Assembler to be used : " }, { "name": "mitoz_assemble_kmers", "prefix": "--kmers", "type": "text", "value": "39 59 79 99 119 141", "label": "kmer size(s) to be used. Multiple kmers can be used, separated by space." }, { "name": "mitoz_assemble_threads", "prefix": "--thread_number", "type": "numeric", "value": 4, "min": 1, "max": "NA", "step": 1, "label": "Number of threads to use" }, { "name": "mitoz_assemble_clade", "type": "radio", "value": "Arthropoda", "choices": [ { "Arthropoda": "Arthropoda" }, { "Chordata": "Chordata" }, { "Echinodermata": "Echinodermata" }, { "Annelida-segmented-worms": "Annelida-segmented-worms" }, { "Bryozoa": "Bryozoa" }, { "Mollusca": "Mollusca" }, { "Nematoda": "Nematoda" }, { "Nemertea-ribbon-worms": "Nemertea-ribbon-worms" }, { "Porifera-sponges": "Porifera-sponges" } ], "label": "Taxa group for MitoZ : " }, { "name": "mitoz_assemble_read_length", "prefix": "--fastq_read_length", "type": "numeric", "value": 150, "min": 50, "max": "NA", "step": 1, "label": "Read length" } ] }, { "name": "mitoz_assemble_PE", "cname": "MitoZ Assemble PE", "command": "mitoz assemble ", "category": "assembly", "output_dir": "mitoz_assemble_PE", "inputs": [ { "name": "read", "type": "reads" }, { "name": "read2", "type": "reads" } ], "outputs": [ { "name": "read_assembled", "type": "contigs", "file": "final.contigs.fa", "description": "Reads assembled" }, { "name": "mitogenome", "type": "contigs", "file": "{assembler}.mitogenome.fa", "description": "mitochondrial sequences found" } ], "options": [ { "name": "mitoz_assemble_assembler", "type": "radio", "value": "megahit", "choices": [ { "megahit": "megahit" }, { "spades": "spades" }, { "mitoassemble": "mitoassemble" } ], "label": "Assembler to be used : " }, { "name": "mitoz_assemble_kmers", "prefix": "--kmers", "type": "text", "value": "39 59 79 99 119 141", "label": "kmer size(s) to be used. Multiple kmers can be used, separated by space." }, { "name": "mitoz_assemble_threads", "prefix": "--thread_number", "type": "numeric", "value": 4, "min": 1, "max": "NA", "step": 1, "label": "Number of threads to use" }, { "name": "mitoz_assemble_clade", "type": "radio", "value": "Arthropoda", "choices": [ { "Arthropoda": "Arthropoda" }, { "Chordata": "Chordata" }, { "Echinodermata": "Echinodermata" }, { "Annelida-segmented-worms": "Annelida-segmented-worms" }, { "Bryozoa": "Bryozoa" }, { "Mollusca": "Mollusca" }, { "Nematoda": "Nematoda" }, { "Nemertea-ribbon-worms": "Nemertea-ribbon-worms" }, { "Porifera-sponges": "Porifera-sponges" } ], "label": "Taxa group for MitoZ : " }, { "name": "mitoz_assemble_read_length", "prefix": "--fastq_read_length", "type": "numeric", "value": 150, "min": 50, "max": "NA", "step": 1, "label": "Read length" }, { "name": "mitoz_assemble_insert_size_PE", "prefix": "--insert_size", "type": "numeric", "value": 250, "min": 0, "max": "NA", "step": 1, "label": "Insert size" } ] } ], "install": [], "citations": { "mitoz": [ "Guanliang Meng, Yiyuan Li, Chentao Yang, Shanlin Liu, MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization, Nucleic Acids Research, , gkz173, https:\/\/doi.org\/10.1093\/nar\/gkz173" ], "megahit": [ "Li, D., Luo, R., Liu, C.-M., Leung, C.-M., Ting, H.-F., Sadakane, K., Yamashita, H., & Lam, T.-W. (2016). MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices. Methods, 102, 3\u201111. https:\/\/doi.org\/10.1016\/j.ymeth.2016.02.020" ], "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: mitoz_assemble,\n name: MitoZ assemble and find mitogenome,\n article: 10.1093\/nar\/gkz173,\n website: \"https:\/\/github.com\/linzhi2013\/MitoZ\",\n git: \"https:\/\/github.com\/linzhi2013\/MitoZ\",\n description: \"A toolkit for assembly, annotation, and visualization of animal mitochondrial genomes\",\n version: \"3.5\",\n documentation: \"https:\/\/github.com\/linzhi2013\/MitoZ\",\n multiqc: \"custom\",\n commands:\n [\n {\n name: mitoz_assemble_SE,\n cname: \"MitoZ Assemble SE\",\n command: \"mitoz assemble \",\n category: \"assembly\",\n output_dir: mitoz_assemble_SE,\n inputs: [{ name: read, type: \"reads\" }],\n outputs:\n [\n { name: read_assembled, type: \"contigs\", file: \"final.contigs.fa\", description: \"Reads assembled\" },\n { name: mitogenome, type: \"contigs\", file: \"{assembler}.mitogenome.fa\", description: \"mitochondrial sequences found\" }\n ],\n options:\n [\n { \n name: \"mitoz_assemble_assembler\",\n type: \"radio\",\n value: \"megahit\",\n choices: [\n megahit: megahit,\n spades: spades, \n mitoassemble: mitoassemble\n ],\n label: \"Assembler to be used : \",\n },\n {\n name: mitoz_assemble_kmers,\n prefix: --kmers,\n type: text,\n value: \"39 59 79 99 119 141\",\n label: \"kmer size(s) to be used. Multiple kmers can be used, separated by space.\",\n }, \n {\n name: mitoz_assemble_threads,\n prefix: --thread_number,\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: \"mitoz_assemble_clade\",\n type: \"radio\",\n value: \"Arthropoda\",\n choices: [\n Arthropoda: Arthropoda,\n Chordata: Chordata, \n Echinodermata: Echinodermata,\n Annelida-segmented-worms: Annelida-segmented-worms,\n Bryozoa: Bryozoa,\n Mollusca: Mollusca,\n Nematoda: Nematoda,\n Nemertea-ribbon-worms: Nemertea-ribbon-worms,\n Porifera-sponges: Porifera-sponges\n ],\n label: \"Taxa group for MitoZ : \",\n },\n {\n name: mitoz_assemble_read_length,\n prefix: --fastq_read_length,\n type: numeric,\n value: 150,\n min: 50,\n max: NA,\n step: 1,\n label: \"Read length\",\n }\n ],\n },\n {\n name: mitoz_assemble_PE,\n cname: \"MitoZ Assemble PE\",\n command: \"mitoz assemble \",\n category: \"assembly\",\n output_dir: mitoz_assemble_PE,\n inputs: [{ name: read, type: \"reads\" }, { name: read2, type: \"reads\" }],\n outputs:\n [\n { name: read_assembled, type: \"contigs\", file: \"final.contigs.fa\", description: \"Reads assembled\" },\n { name: mitogenome, type: \"contigs\", file: \"{assembler}.mitogenome.fa\", description: \"mitochondrial sequences found\" }\n ],\n options:\n [\n { name: \"mitoz_assemble_assembler\",\n type: \"radio\",\n value: \"megahit\",\n choices: [\n megahit: megahit,\n spades: spades, \n mitoassemble: mitoassemble\n ],\n label: \"Assembler to be used : \",\n },\n {\n name: mitoz_assemble_kmers,\n prefix: --kmers,\n type: text,\n value: \"39 59 79 99 119 141\",\n label: \"kmer size(s) to be used. Multiple kmers can be used, separated by space.\",\n }, \n {\n name: mitoz_assemble_threads,\n prefix: --thread_number,\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: \"mitoz_assemble_clade\",\n type: \"radio\",\n value: \"Arthropoda\",\n choices: [\n Arthropoda: Arthropoda,\n Chordata: Chordata, \n Echinodermata: Echinodermata,\n Annelida-segmented-worms: Annelida-segmented-worms,\n Bryozoa: Bryozoa,\n Mollusca: Mollusca,\n Nematoda: Nematoda,\n Nemertea-ribbon-worms: Nemertea-ribbon-worms,\n Porifera-sponges: Porifera-sponges\n ],\n label: \"Taxa group for MitoZ : \",\n },\n {\n name: mitoz_assemble_read_length,\n prefix: --fastq_read_length,\n type: numeric,\n value: 150,\n min: 50,\n max: NA,\n step: 1,\n label: \"Read length\",\n },\n {\n name: mitoz_assemble_insert_size_PE,\n prefix: --insert_size,\n type: numeric,\n value: 250,\n min: 0,\n max: NA,\n step: 1,\n label: \"Insert size\",\n },\n\n ],\n },\n ],\n install: {\n # mitoz3.5: [\n # \"cd \/opt\/biotools\",\n # \"singularity pull MitoZ_v3.5.sif docker:\/\/guanliangmeng\/mitoz:3.5\",\n # ]\n \n },\n citations: {\n mitoz: [\n \"Guanliang Meng, Yiyuan Li, Chentao Yang, Shanlin Liu, MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization, Nucleic Acids Research, , gkz173, https:\/\/doi.org\/10.1093\/nar\/gkz173\"\n ],\n megahit: [\n \"Li, D., Luo, R., Liu, C.-M., Leung, C.-M., Ting, H.-F., Sadakane, K., Yamashita, H., & Lam, T.-W. (2016). MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices. Methods, 102, 3\u201111. https:\/\/doi.org\/10.1016\/j.ymeth.2016.02.020\"\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}" } ]