[ { "id": "bwa_mem", "name": "BWA MEM (Burrows-Wheeler Alignment Tool)", "article": "10.1093\/bioinformatics\/btp324", "website": "http:\/\/bio-bwa.sourceforge.net\/", "git": "https:\/\/github.com\/lh3\/bwa", "description": "BWA is a software package for mapping low-divergent sequences against a large reference genome.", "version": "0.7.17", "documentation": "http:\/\/bio-bwa.sourceforge.net\/bwa.shtml", "multiqc": "custom", "commands": [ { "name": "bwa_mem_PE", "cname": "Bwa mem PE", "command": "bwa mem", "category": "mapping", "output_dir": "bwa\/mem\/PE", "inputs": [ { "name": "read", "type": "reads" }, { "name": "read2", "type": "reads" }, { "name": "index", "type": "bwa_mem_index", "file": "index", "description": "Index files for bwa alignment" } ], "outputs": [ { "name": "bam", "type": "bams", "file": "{sample}.bam", "description": "Alignment files" } ], "options": [ { "name": "bwa_mem_threads", "prefix": "-t", "type": "numeric", "value": 4, "min": 1, "max": "NA", "step": 1, "label": "Number of threads to use" }, { "name": "bwa_mem_quality0_multimapping", "prefix": null, "type": "checkbox", "value": true, "label": "Put 0 as mapping quality for multimapping reads" } ] }, { "name": "bwa_mem_SE", "cname": "Bwa mem SE", "command": "bwa mem", "category": "mapping", "output_dir": "bwa\/mem\/SE", "inputs": [ { "name": "read", "type": "reads" }, { "name": "index", "type": "bwa_mem_index", "file": "index", "description": "Index files for bwa alignment" } ], "outputs": [ { "name": "bam", "type": "bams", "file": "{sample}.bam", "description": "Alignment files" } ], "options": [ { "name": "bwa_mem_threads", "prefix": "-t", "type": "numeric", "value": 4, "min": 1, "max": "NA", "step": 1, "label": "Number of threads to use" }, { "name": "bwa_mem_quality0_multimapping", "prefix": null, "type": "checkbox", "value": true, "label": "Put 0 as mapping quality for multimapping reads" } ] } ], "install": [], "citations": { "bwa": [ "Heng Li, Richard Durbin, Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, Volume 25, Issue 14, 15 July 2009, Pages 1754-1760, https:\/\/doi.org\/10.1093\/bioinformatics\/btp324" ], "bwa-mem": [ "Li H. (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997v1 [q-bio.GN]" ], "samtools": [ "Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup, The Sequence Alignment\/Map format and SAMtools, Bioinformatics, Volume 25, Issue 16, 15 August 2009, Pages 2078-2079, https:\/\/doi.org\/10.1093\/bioinformatics\/btp352" ] }, "yaml": "{\n id: bwa_mem,\n name: BWA MEM (Burrows-Wheeler Alignment Tool),\n article: 10.1093\/bioinformatics\/btp324,\n website: \"http:\/\/bio-bwa.sourceforge.net\/\",\n git: \"https:\/\/github.com\/lh3\/bwa\",\n description: \"BWA is a software package for mapping low-divergent sequences against a large reference genome.\",\n version: \"0.7.17\",\n documentation: \"http:\/\/bio-bwa.sourceforge.net\/bwa.shtml\",\n multiqc: \"custom\",\n commands:\n [\n {\n name: bwa_mem_PE,\n cname: \"Bwa mem PE\",\n command: bwa mem,\n category: \"mapping\",\n output_dir: bwa\/mem\/PE,\n inputs: [{ name: read, type: \"reads\" }, { name: read2, type: \"reads\" }, { name: index, type: \"bwa_mem_index\", file: index, description: \"Index files for bwa alignment\" }],\n outputs: [{ name: bam, type: \"bams\", file: \"{sample}.bam\", description: \"Alignment files\" }],\n options:\n [\n {\n name: bwa_mem_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: bwa_mem_quality0_multimapping,\n prefix: ,\n type: checkbox,\n value: TRUE,\n label: \"Put 0 as mapping quality for multimapping reads\",\n }\n ],\n },\n {\n name: bwa_mem_SE,\n cname: \"Bwa mem SE\",\n command: bwa mem,\n category: \"mapping\",\n output_dir: bwa\/mem\/SE,\n inputs: [{ name: read, type: \"reads\" }, { name: index, type: \"bwa_mem_index\", file: index, description: \"Index files for bwa alignment\" }],\n outputs: [{ name: bam, type: \"bams\", file: \"{sample}.bam\", description: \"Alignment files\" }],\n options:\n [\n {\n name: bwa_mem_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: bwa_mem_quality0_multimapping,\n prefix: ,\n type: checkbox,\n value: TRUE,\n label: \"Put 0 as mapping quality for multimapping reads\",\n }\n ],\n }\n ],\n install: {\n # bwa: [\n # \"cd \/opt\/biotools\",\n # \"wget https:\/\/github.com\/lh3\/bwa\/releases\/download\/v0.7.17\/bwa-0.7.17.tar.bz2\",\n # \"tar -xvjf bwa-0.7.17.tar.bz2\",\n # \"cd bwa-0.7.17\",\n # \"make -j 10\",\n # \"mv bwa ..\/bin\/\",\n # \"cd ..\",\n # \"rm -r bwa-0.7.17 bwa-0.7.17.tar.bz2\"\n # ],\n # samtools: [\n # \"cd \/opt\/biotools\",\n # \"wget https:\/\/github.com\/samtools\/samtools\/releases\/download\/1.9\/samtools-1.9.tar.bz2\",\n # \"tar -xvjf samtools-1.9.tar.bz2\",\n # \"cd samtools-1.9\",\n # \".\/configure && make\",\n # \"cd ..\",\n # \"mv samtools-1.9\/samtools bin\/samtools\",\n # \"rm -r samtools-1.9 samtools-1.9.tar.bz2\"\n # ]\n },\n citations: {\n bwa: [\n \"Heng Li, Richard Durbin, Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, Volume 25, Issue 14, 15 July 2009, Pages 1754-1760, https:\/\/doi.org\/10.1093\/bioinformatics\/btp324\"\n ],\n bwa-mem: [\n \"Li H. (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997v1 [q-bio.GN]\"\n ],\n samtools: [\n \"Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup, The Sequence Alignment\/Map format and SAMtools, Bioinformatics, Volume 25, Issue 16, 15 August 2009, Pages 2078-2079, https:\/\/doi.org\/10.1093\/bioinformatics\/btp352\"\n ]\n }\n}" } ]