[ { "id": "abyss", "name": "ABySS", "description": "ABySS is a de novo sequence assembler intended for short paired-end reads and large genomes.", "version": "2.3.7", "website": "https:\/\/www.bcgsc.ca\/resources\/software\/abyss", "git": "https:\/\/github.com\/bcgsc\/abyss", "documentation": "https:\/\/github.com\/bcgsc\/abyss\/blob\/master\/README.md", "article": "10.1101\/gr.214346.116", "multiqc": "custom", "commands": [ { "name": "abyss_PE", "cname": "ABySS PE", "category": "assembly", "command": "abyss-pe", "output_dir": "abyss", "inputs": [ { "name": "read", "type": "reads" }, { "name": "read2", "type": "reads" } ], "outputs": [ { "name": "contigs", "file": "out-contigs.fa", "type": "contigs", "description": "Assembled contigs" }, { "name": "mqc_stats", "file": "ABySS_stats_mqc.csv", "type": "csv", "description": "Assembly stats" } ], "options": [ { "name": "abyss_PE_threads", "prefix": "j=", "value": 2, "min": 1, "max": 60, "step": 1, "label": "Specify the number (N=integer) of threads\/cores ", "type": "numeric" }, { "name": "abyss_PE_k", "prefix": "k=", "value": 64, "min": 32, "max": 128, "step": 1, "label": "-k: size of k-mer", "type": "numeric" }, { "name": "abyss_PE_B", "prefix": "B=", "value": 6, "min": 1, "max": 500, "step": 1, "label": "B= Bloom filter mode define the bloom memory budget (in gigabytes).", "type": "numeric" }, { "name": "abyss_PE_l", "prefix": "l=", "value": 40, "min": 0, "max": "NA", "step": 1, "label": "-l: minimum alignment length of a read (bp)", "type": "numeric" }, { "name": "abyss_PE_q", "prefix": "q=", "value": 3, "min": 0, "max": "NA", "step": 1, "label": "-q: minimum base quality when trimming (Trim bases from the ends of reads whose quality is less q)", "type": "numeric" }, { "name": "abyss_PE_n", "prefix": "n=", "value": 10, "min": 0, "max": "NA", "step": 1, "label": "-n: minimum number of pairs required for building contigs", "type": "numeric" }, { "name": "abyss_PE_other_options", "value": "", "label": "Options to add to the command line", "type": "text" } ] } ], "install": [], "citations": { "abyss": [ "Shaun D Jackman, Benjamin P Vandervalk, Hamid Mohamadi, Justin Chu, Sarah Yeo, S Austin Hammond, Golnaz Jahesh, Hamza Khan, Lauren Coombe, Ren\u00e9 L Warren, and Inanc Birol (2017). ABySS 2.0: Resource-efficient assembly of large genomes using a Bloom filter. Genome research, 27(5), 768-777. doi:10.1101\/gr.214346.116" ] }, "yaml": "{\n id: \"abyss\",\n name: \"ABySS\",\n description: \"ABySS is a de novo sequence assembler intended for short paired-end reads and large genomes.\",\n version: \"2.3.7\",\n website: \"https:\/\/www.bcgsc.ca\/resources\/software\/abyss\",\n git: \"https:\/\/github.com\/bcgsc\/abyss\",\n documentation: \"https:\/\/github.com\/bcgsc\/abyss\/blob\/master\/README.md\",\n article: \"10.1101\/gr.214346.116\",\n multiqc: \"custom\",\n commands:\n [\n {\n name: \"abyss_PE\",\n cname: \"ABySS PE\",\n category: \"assembly\",\n command: \"abyss-pe\",\n output_dir: \"abyss\",\n inputs:\n [\n { name: \"read\", type: \"reads\" },\n { name: \"read2\", type: \"reads\" },\n ],\n outputs: [\n {\n name: \"contigs\",\n file: \"out-contigs.fa\",\n type: \"contigs\",\n description: \"Assembled contigs\",\n },\n {\n name: \"mqc_stats\",\n file: \"ABySS_stats_mqc.csv\",\n type: \"csv\",\n description: \"Assembly stats\",\n },\n ],\n options:\n [\n {\n name: \"abyss_PE_threads\",\n prefix: \"j=\",\n value: 2,\n min: 1,\n max: 60,\n step: 1,\n label: \"Specify the number (N=integer) of threads\/cores \",\n type: \"numeric\",\n },\n {\n name: \"abyss_PE_k\",\n prefix: \"k=\",\n value: 64,\n min: 32,\n max: 128,\n step: 1,\n label: \"-k: size of k-mer\",\n type: \"numeric\",\n },\n {\n name: \"abyss_PE_B\",\n prefix: \"B=\",\n value: 6,\n min: 1,\n max: 500,\n step: 1,\n label: \"B= Bloom filter mode define the bloom memory budget (in gigabytes).\",\n type: \"numeric\",\n },\n {\n name: \"abyss_PE_l\",\n prefix: \"l=\",\n value: 40,\n min: 0,\n max: NA,\n step: 1,\n label: \"-l: minimum alignment length of a read (bp)\",\n type: \"numeric\",\n },\n {\n name: \"abyss_PE_q\",\n prefix: \"q=\",\n value: 3,\n min: 0,\n max: NA,\n step: 1,\n label: \"-q: minimum base quality when trimming (Trim bases from the ends of reads whose quality is less q)\",\n type: \"numeric\",\n },\n {\n name: \"abyss_PE_n\",\n prefix: \"n=\",\n value: 10,\n min: 0,\n max: NA,\n step: 1,\n label: \"-n: minimum number of pairs required for building contigs\",\n type: \"numeric\",\n },\n {\n name: \"abyss_PE_other_options\",\n value: \"\",\n label: \"Options to add to the command line\",\n type: \"text\",\n },\n ],\n },\n ],\n install:\n {\n # abyss: [\n # \"apt-get update\",\n # \"apt-get install -y libboost-dev libopenmpi-dev libsparsehash-dev bsdmainutils\",\n # \"cd \/opt\/biotools\",\n # \"wget https:\/\/github.com\/bcgsc\/abyss\/archive\/2.2.5.tar.gz\",\n # \"tar -xvzf 2.2.5.tar.gz\",\n # \"rm 2.2.5.tar.gz\",\n # \"cd abyss-2.2.5\",\n # \".\/autogen.sh\",\n # \"mkdir build && cd build\",\n # \"..\/configure\",\n # \"make install-strip\"\n # ],\n },\n citations:\n {\n abyss: [\n \"Shaun D Jackman, Benjamin P Vandervalk, Hamid Mohamadi, Justin Chu, Sarah Yeo, S Austin Hammond, Golnaz Jahesh, Hamza Khan, Lauren Coombe, Ren\u00e9 L Warren, and Inanc Birol (2017). ABySS 2.0: Resource-efficient assembly of large genomes using a Bloom filter. Genome research, 27(5), 768-777. doi:10.1101\/gr.214346.116\",\n ],\n },\n}\n" } ]