[ { "id": "get_organelle", "name": "GetOrganelle", "description": "This toolkit assembles organelle genome from genomic skimming data.", "version": "1.7.7.0", "website": "https:\/\/github.com\/Kinggerm\/GetOrganelle", "git": "https:\/\/github.com\/Kinggerm\/GetOrganelle", "documentation": "https:\/\/github.com\/Kinggerm\/GetOrganelle\/wiki", "article": "10.1186\/s13059-020-02154-5", "multiqc": "custom", "commands": [ { "name": "get_organelle_SE", "cname": "get_organelle SE", "output_dir": "get_organelle_SE", "category": "find_mito_scaffold", "command": "get_organelle_from_reads.py", "inputs": [ { "name": "read", "file": "", "type": "reads", "description": "" } ], "outputs": [ { "name": "assembly", "file": "assembly.fasta", "type": "contigs", "description": "Assembly fasta file" } ], "options": [ { "name": "get_organelle_SE_threads", "prefix": "-t", "type": "numeric", "value": 8, "min": 1, "max": "NA", "step": 1, "label": "Number of threads to use" }, { "name": "get_organelle_SE_organelle_type", "prefix": "-F", "type": "select", "choices": [ { "embryophyta plant plastome": "embplant_pt" }, { "non-embryophyta plant plastome": "other_pt" }, { "plant mitogenome": "embplant_mt" }, { "plant nuclear ribosomal RNA": "embplant_nr" }, { "animal mitogenome": "animal_mt" }, { "fungus mitogenome": "fungus_mt" } ], "value": "animal_mt", "label": "Organelle type" }, { "name": "get_organelle_SE_max_rounds", "prefix": "-R", "type": "numeric", "value": 15, "min": 2, "max": "NA", "step": 1, "label": "Maximum number of extending rounds (suggested: >=2)" } ] }, { "name": "get_organelle_PE", "cname": "get_organelle PE", "output_dir": "get_organelle_PE", "category": "find_mito_scaffold", "command": "get_organelle_from_reads.py", "inputs": [ { "name": "read", "type": "reads" }, { "name": "read2", "type": "reads" } ], "outputs": [ { "name": "assembly", "file": "assembly.fasta", "type": "contigs", "description": "Assembly fasta file" } ], "options": [ { "name": "get_organelle_PE_threads", "prefix": "-t", "type": "numeric", "value": 8, "min": 1, "max": "NA", "step": 1, "label": "Number of threads to use" }, { "name": "get_organelle_PE_organelle_type", "type": "select", "prefix": "-F", "choices": [ { "embryophyta plant plastome": "embplant_pt" }, { "non-embryophyta plant plastome": "other_pt" }, { "plant mitogenome": "embplant_mt" }, { "plant nuclear ribosomal RNA": "embplant_nr" }, { "animal mitogenome": "animal_mt" }, { "fungus mitogenome": "fungus_mt" } ], "value": "animal_mt", "label": "Organelle type" }, { "name": "get_organelle_PE_max_rounds", "prefix": "-R", "type": "numeric", "value": 15, "min": 2, "max": "NA", "step": 1, "label": "Maximum number of extending rounds (suggested: >=2)" } ] } ], "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." ], "bowtie2": [ "Langmead, B. and S. L. Salzberg. 2012. Fast gapped-read alignment with Bowtie 2. Nature Methods 9: 357-359." ], "blast": [ "Camacho, C., G. Coulouris, V. Avagyan, N. Ma, J. Papadopoulos, K. Bealer and T. L. Madden. 2009. BLAST+: architecture and applications. BMC Bioinformatics 10: 421." ], "bandage": [ "Wick, R. R., M. B. Schultz, J. Zobel and K. E. Holt. 2015. Bandage: interactive visualization of de novo genome assemblies. Bioinformatics 31: 3350-3352." ], "get_organelle": [ "Jian-Jun Jin*, Wen-Bin Yu*, Jun-Bo Yang, Yu Song, Claude W. dePamphilis, Ting-Shuang Yi, De-Zhu Li. GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biology 21, 241 (2020). https:\/\/doi.org\/10.1186\/s13059-020-02154-5" ] }, "yaml": "{\n id: \"get_organelle\",\n name: \"GetOrganelle\",\n description: \"This toolkit assembles organelle genome from genomic skimming data.\",\n version: \"1.7.7.0\",\n website: \"https:\/\/github.com\/Kinggerm\/GetOrganelle\",\n git: \"https:\/\/github.com\/Kinggerm\/GetOrganelle\",\n documentation: \"https:\/\/github.com\/Kinggerm\/GetOrganelle\/wiki\",\n article: \"10.1186\/s13059-020-02154-5\", # DOI\n multiqc: \"custom\",\n commands:\n [\n {\n name: \"get_organelle_SE\",\n cname: \"get_organelle SE\",\n output_dir: \"get_organelle_SE\",\n category: \"find_mito_scaffold\",\n command: \"get_organelle_from_reads.py\",\n inputs: [\n {\n name: \"read\",\n file: \"\",\n type: \"reads\",\n description: \"\"\n }\n ],\n outputs: [\n {\n name: \"assembly\",\n file: \"assembly.fasta\",\n type: \"contigs\",\n description: \"Assembly fasta file\"\n }\n ],\n options:\n [\n {\n name: \"get_organelle_SE_threads\",\n prefix: \"-t\",\n type: \"numeric\",\n value: 8,\n min: 1,\n max: NA,\n step: 1,\n label: \"Number of threads to use\"\n },\n {\n name: \"get_organelle_SE_organelle_type\",\n prefix: \"-F\",\n type: \"select\",\n choices: [\n embryophyta plant plastome : \"embplant_pt\",\n non-embryophyta plant plastome : \"other_pt\",\n plant mitogenome : \"embplant_mt\",\n plant nuclear ribosomal RNA : \"embplant_nr\",\n animal mitogenome : \"animal_mt\",\n fungus mitogenome : \"fungus_mt\"\n ],\n value: \"animal_mt\",\n label: \"Organelle type\"\n },\n {\n name: \"get_organelle_SE_max_rounds\",\n prefix: \"-R\",\n type: \"numeric\",\n value: 15,\n min: 2,\n max: NA,\n step: 1,\n label: \"Maximum number of extending rounds (suggested: >=2)\"\n },\n ],\n },\n {\n name: \"get_organelle_PE\",\n cname: \"get_organelle PE\",\n output_dir: \"get_organelle_PE\",\n category: \"find_mito_scaffold\",\n command: \"get_organelle_from_reads.py\",\n inputs: [\n {\n name: \"read\",\n type: \"reads\",\n },\n {\n name: \"read2\",\n type: \"reads\",\n }\n ],\n outputs: [\n {\n name: \"assembly\",\n file: \"assembly.fasta\",\n type: \"contigs\",\n description: \"Assembly fasta file\"\n },\n ],\n options: [\n {\n name: \"get_organelle_PE_threads\",\n prefix: \"-t\",\n type: \"numeric\",\n value: 8,\n min: 1,\n max: NA,\n step: 1,\n label: \"Number of threads to use\",\n },\n {\n name: \"get_organelle_PE_organelle_type\",\n type: \"select\",\n prefix: \"-F\",\n choices: [\n embryophyta plant plastome : \"embplant_pt\",\n non-embryophyta plant plastome : \"other_pt\",\n plant mitogenome : \"embplant_mt\",\n plant nuclear ribosomal RNA : \"embplant_nr\",\n animal mitogenome : \"animal_mt\",\n fungus mitogenome : \"fungus_mt\",\n ],\n value: \"animal_mt\",\n label: \"Organelle type\"\n },\n {\n name: \"get_organelle_PE_max_rounds\",\n prefix: \"-R\",\n type: \"numeric\",\n value: 15,\n min: 2,\n max: NA,\n step: 1,\n label: \"Maximum number of extending rounds (suggested: >=2)\",\n },\n ]\n }\n ],\n install: {\n # spades:\n # [\n # \"cd \/opt\/biotools\",\n # \"wget http:\/\/cab.spbu.ru\/files\/release3.14.1\/SPAdes-3.14.1-Linux.tar.gz\",\n # \"tar -xvzf SPAdes-3.14.1-Linux.tar.gz\",\n # \"ENV PATH $PATH:\/opt\/biotools\/SPAdes-3.14.1-Linux\/bin\",\n # \"rm SPAdes-3.14.1-Linux.tar.gz\"\n # ],\n # bowtie2:\n # [\n # \"wget -O bowtie2-2.4.1-linux-x86_64.zip https:\/\/github.com\/BenLangmead\/bowtie2\/releases\/download\/v2.4.1\/bowtie2-2.4.1-linux-x86_64.zip\",\n # \"unzip bowtie2-2.4.1-linux-x86_64.zip\",\n # \"cp bowtie2-2.4.1-linux-x86_64\/bowtie2* \/usr\/bin\",\n # \"rm -rf bowtie2-2.4.1*\"\n # ],\n # blast: \n # [\n # \"cd \/opt\/biotools\/\",\n # \"wget -O ncbi-blast-2.10.1+.tar.gz https:\/\/ftp.ncbi.nlm.nih.gov\/blast\/executables\/blast+\/2.10.1\/ncbi-blast-2.10.1+-x64-linux.tar.gz\",\n # \"tar -xvzf ncbi-blast-2.10.1+.tar.gz\",\n # \"ENV PATH $PATH:\/opt\/biotools\/ncbi-blast-2.10.1+\/bin\"\n # ],\n # bandage:\n # [\n # \"cd \/opt\/biotools\",\n # \"wget https:\/\/github.com\/rrwick\/Bandage\/releases\/download\/v0.8.1\/Bandage_Ubuntu_static_v0_8_1.zip\",\n # \"unzip -d bandage Bandage_Ubuntu_static_v0_8_1.zip\",\n # \"mv bandage\/Bandage bin\/\",\n # \"rm -r bandage Bandage_Ubuntu_static_v0_8_1.zip\"\n # ],\n # get_organelle:\n # [\n # \"cd \/opt\/biotools\",\n # \"wget -O GetOrganelle-1.7.5.3.tar.gz https:\/\/codeload.github.com\/Kinggerm\/GetOrganelle\/tar.gz\/refs\/tags\/1.7.5.3\",\n # \"tar -xvzf GetOrganelle-1.7.5.3.tar.gz --no-same-owner \",\n # \"mv GetOrganelle-1.7.5.3 GetOrganelle \",\n # \"cd GetOrganelle && python setup.py install \",\n # \"cd .. && rm GetOrganelle-1.7.5.3.tar.gz \",\n # \"get_organelle_config.py -a all\"\n # ]\n },\n citations: {\n spades: \n [\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 bowtie2:\n [\n \"Langmead, B. and S. L. Salzberg. 2012. Fast gapped-read alignment with Bowtie 2. Nature Methods 9: 357-359.\"\n ],\n blast:\n [\n \"Camacho, C., G. Coulouris, V. Avagyan, N. Ma, J. Papadopoulos, K. Bealer and T. L. Madden. 2009. BLAST+: architecture and applications. BMC Bioinformatics 10: 421.\"\n ],\n bandage:\n [\n \"Wick, R. R., M. B. Schultz, J. Zobel and K. E. Holt. 2015. Bandage: interactive visualization of de novo genome assemblies. Bioinformatics 31: 3350-3352.\"\n ],\n get_organelle:\n [\n \"Jian-Jun Jin*, Wen-Bin Yu*, Jun-Bo Yang, Yu Song, Claude W. dePamphilis, Ting-Shuang Yi, De-Zhu Li. GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biology 21, 241 (2020). https:\/\/doi.org\/10.1186\/s13059-020-02154-5\"\n ]\n }\n}\n" } ]