[ { "id": "megahit", "name": "MEGAHIT", "article": "10.1016\/j.ymeth.2016.02.020", "website": "https:\/\/github.com\/voutcn\/megahit", "git": "https:\/\/github.com\/voutcn\/megahit", "description": "An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph", "version": "1.2.9", "documentation": "https:\/\/github.com\/voutcn\/megahit\/wiki", "multiqc": "custom", "commands": [ { "name": "megahit_SE", "cname": "Megahit SE", "command": "megahit", "category": "assembly", "output_dir": "megahit_SE", "inputs": [ { "name": "read", "type": "reads" } ], "outputs": [ { "name": "contigs", "type": "contigs", "file": "assembly.contigs.fa", "description": "Result of the assembly" } ], "options": [ { "name": "megahit_threads", "prefix": "-t", "type": "numeric", "value": 4, "min": 1, "max": "NA", "step": 1, "label": "Number of threads to use" }, { "name": "megahit_min_contig_len", "prefix": "--min-contig-len", "type": "numeric", "value": 200, "min": 1, "max": "NA", "step": 1, "label": "Minimum length of contigs to output" } ] }, { "name": "megahit_PE", "cname": "Megahit PE", "command": "megahit", "category": "assembly", "output_dir": "megahit_PE", "inputs": [ { "name": "read", "type": "reads" }, { "name": "read2", "type": "reads" } ], "outputs": [ { "name": "contigs", "type": "contigs", "file": "assembly.contigs.fa", "description": "Result of the assembly" } ], "options": [ { "name": "megahit_threads", "prefix": "-t", "type": "numeric", "value": 4, "min": 1, "max": "NA", "step": 1, "label": "Number of threads to use" }, { "name": "megahit_min_contig_len", "prefix": "--min-contig-len", "type": "numeric", "value": 200, "min": 1, "max": "NA", "step": 1, "label": "Minimum length of contigs to output" }, { "name": "megahit_minKmer", "prefix": "--k-min", "type": "numeric", "value": 21, "min": 1, "max": 255, "step": 2, "label": "minimum kmer size (<= 255), must be odd number" }, { "name": "megahit_maxKmer", "prefix": "--k-max", "type": "numeric", "value": 141, "min": 1, "max": 255, "step": 2, "label": "maximum kmer size (<= 255), must be odd number" }, { "name": "megahit_Kstep", "prefix": "--k-step", "type": "numeric", "value": 12, "min": 1, "max": 28, "step": 2, "label": "increment of kmer size of each iteration (<= 28), must be even number" } ] } ], "prepare_report_script": "megahit.prepare.report.py", "prepare_report_outputs": [ "Assembly_stats_mqc.tsv" ], "install": [], "citations": { "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" ] }, "yaml": "{\n id: megahit,\n name: MEGAHIT,\n article: \"10.1016\/j.ymeth.2016.02.020\",\n website: \"https:\/\/github.com\/voutcn\/megahit\",\n git: \"https:\/\/github.com\/voutcn\/megahit\",\n description: \"An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph\",\n version: \"1.2.9\",\n documentation: \"https:\/\/github.com\/voutcn\/megahit\/wiki\",\n multiqc: \"custom\",\n commands:\n [\n {\n name: megahit_SE,\n cname: \"Megahit SE\",\n command: megahit,\n category: \"assembly\",\n output_dir: megahit_SE,\n inputs: [{ name: read, type: \"reads\" }],\n outputs:\n [\n { name: contigs, type: \"contigs\", file: \"assembly.contigs.fa\", description: \"Result of the assembly\" },\n ],\n options:\n [\n {\n name: megahit_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: megahit_min_contig_len,\n prefix: --min-contig-len,\n type: numeric,\n value: 200,\n min: 1,\n max: NA,\n step: 1,\n label: \"Minimum length of contigs to output\",\n },\n ],\n },\n {\n name: megahit_PE,\n cname: \"Megahit PE\",\n command: megahit,\n category: \"assembly\",\n output_dir: megahit_PE,\n inputs: [{ name: read, type: \"reads\" }, { name: read2, type: \"reads\" }],\n outputs:\n [\n { name: contigs, type: \"contigs\", file: \"assembly.contigs.fa\", description: \"Result of the assembly\" },\n ],\n options:\n [\n {\n name: megahit_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: megahit_min_contig_len,\n prefix: --min-contig-len,\n type: numeric,\n value: 200,\n min: 1,\n max: NA,\n step: 1,\n label: \"Minimum length of contigs to output\",\n },\n {\n name: megahit_minKmer,\n prefix: --k-min,\n type: numeric,\n value: 21,\n min: 1,\n max: 255,\n step: 2,\n label: \"minimum kmer size (<= 255), must be odd number\",\n },\n {\n name: megahit_maxKmer,\n prefix: --k-max,\n type: numeric,\n value: 141,\n min: 1,\n max: 255,\n step: 2,\n label: \"maximum kmer size (<= 255), must be odd number\",\n },\n {\n name: megahit_Kstep,\n prefix: --k-step,\n type: numeric,\n value: 12,\n min: 1,\n max: 28,\n step: 2,\n label: \"increment of kmer size of each iteration (<= 28), must be even number\",\n },\n ],\n },\n ],\n prepare_report_script: megahit.prepare.report.py,\n\n prepare_report_outputs: [\n Assembly_stats_mqc.tsv,\n ], \n install: {\n # megahit: [\n # \"cd \/opt\/biotools\",\n # \"git clone https:\/\/github.com\/voutcn\/megahit.git\",\n # \"cd megahit\",\n # \"git submodule update --init\",\n # \"mkdir build && cd build\",\n # \"cmake .. -DCMAKE_BUILD_TYPE=Release\",\n # \"make -j8\",\n # \"make simple_test\",\n # \"make install\",\n # \"cd \/opt\/biotools\",\n # \"rm -rf megahit\"\n # ]\n },\n citations: {\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 }\n}" } ]