[ { "id": "bowtie", "name": "Bowtie", "article": "10.1002\/0471250953.bi1107s32", "website": "http:\/\/bowtie-bio.sourceforge.net", "git": "https:\/\/github.com\/BenLangmead\/bowtie", "description": "Bowtie is an ultrafast, memory-efficient short read aligner.", "version": "1.3.1", "documentation": "http:\/\/bowtie-bio.sourceforge.net\/manual.shtml", "multiqc": "bowtie1", "commands": [ { "name": "bowtie_PE", "cname": "Bowtie PE", "command": "bowtie", "category": "mapping", "output_dir": "bowtie\/PE", "inputs": [ { "name": "read", "type": "reads" }, { "name": "read2", "type": "reads" }, { "name": "index", "type": "bowtie_index", "file": "index", "description": "Index files for bowtie alignment" } ], "outputs": [ { "name": "bam", "type": "bams", "file": "{sample}.bam", "description": "Alignment files" } ], "options": [ { "name": "bowtie_threads", "prefix": "--threads", "type": "numeric", "value": 4, "min": 1, "max": "NA", "step": 1, "label": "Number of threads to use to align reads" }, { "name": "bowtie_minins_PE", "prefix": "-I", "type": "numeric", "value": 0, "min": 0, "max": "NA", "step": 1, "label": "The minimum insert size for valid paired-end alignments" }, { "name": "bowtie_maxins_PE", "prefix": "-X", "type": "numeric", "value": 250, "min": 0, "max": "NA", "step": 1, "label": "The maximum insert size for valid paired-end alignments" }, { "name": "bowtie_orientation_PE", "type": "radio", "choices": [ { "Not stranded": "" }, { "Forward Reverse": "--fr" }, { "Reverse Forward": "--rf" }, { "Forward Forward": "--ff" } ], "value": "", "label": "The upstream\/downstream mate orientations for a valid paired-end alignment against the forward reference strand." }, { "name": "bowtie_mult_align_limit", "prefix": "-m", "type": "numeric", "value": 1, "min": 1, "max": 10, "step": 1, "label": "Suppress all alignments for a particular read or pair if more than 'x' reportable alignments exist for it" }, { "name": "bowtie_best", "prefix": null, "type": "checkbox", "value": true, "label": "--best : Make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum (i.e. number of mismatches, or mismatches in the seed in the case of -n mode) and in terms of the quality values at the mismatched position(s)." }, { "name": "bowtie_strata", "prefix": null, "type": "checkbox", "value": true, "label": "--strata : If many valid alignments exist and are reportable (e.g. are not disallowed via the -k option) and they fall into more than one alignment 'stratum', report only those alignments that fall into the best stratum. When --strata is specified, --best must also be specified." } ] }, { "name": "bowtie_SE", "cname": "Bowtie SE", "command": "bowtie", "category": "mapping", "output_dir": "bowtie\/SE", "inputs": [ { "name": "read", "type": "reads" }, { "name": "index", "type": "bowtie_index", "file": "index", "description": "Index files for bowtie alignment" } ], "outputs": [ { "name": "bam", "type": "bams", "file": "{sample}.bam", "description": "Alignment files" } ], "options": [ { "name": "bowtie_threads", "prefix": "--threads", "type": "numeric", "value": 4, "min": 1, "max": "NA", "step": 1, "label": "Number of threads to use to align reads" }, { "name": "bowtie_mult_align_limit", "prefix": "-m", "type": "numeric", "value": 1, "min": 1, "max": 10, "step": 1, "label": "Suppress all alignments for a particular read or pair if more than 'x' reportable alignments exist for it" }, { "name": "bowtie_best", "prefix": null, "type": "checkbox", "value": true, "label": "--best : Make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum (i.e. number of mismatches, or mismatches in the seed in the case of -n mode) and in terms of the quality values at the mismatched position(s)." }, { "name": "bowtie_strata", "prefix": null, "type": "checkbox", "value": true, "label": "--strata : If many valid alignments exist and are reportable (e.g. are not disallowed via the -k option) and they fall into more than one alignment 'stratum', report only those alignments that fall into the best stratum. When --strata is specified, --best must also be specified." } ] } ], "install": [], "citations": { "bowtie": [ "Langmead, B., Trapnell, C., Pop, M. et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25 (2009). https:\/\/doi.org\/10.1186\/gb-2009-10-3-r25" ], "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: bowtie,\n name: Bowtie,\n article: 10.1002\/0471250953.bi1107s32,\n website: \"http:\/\/bowtie-bio.sourceforge.net\",\n git: \"https:\/\/github.com\/BenLangmead\/bowtie\",\n description: \"Bowtie is an ultrafast, memory-efficient short read aligner.\",\n version: \"1.3.1\",\n documentation: \"http:\/\/bowtie-bio.sourceforge.net\/manual.shtml\",\n multiqc: \"bowtie1\",\n commands:\n [\n {\n name: bowtie_PE,\n cname: \"Bowtie PE\",\n command: bowtie,\n category: \"mapping\",\n output_dir: bowtie\/PE,\n inputs: [{ name: read, type: reads }, { name: read2, type: reads }, { name: index, type: \"bowtie_index\", file: index, description: \"Index files for bowtie alignment\" }],\n outputs: [{ name: bam, type: bams, file: \"{sample}.bam\", description: \"Alignment files\" }],\n options:\n [\n {\n name: bowtie_threads,\n prefix: --threads,\n type: numeric,\n value: 4,\n min: 1,\n max: NA,\n step: 1,\n label: \"Number of threads to use to align reads\",\n },\n {\n name: bowtie_minins_PE,\n prefix: -I,\n type: numeric,\n value: 0,\n min: 0,\n max: NA,\n step: 1,\n label: \"The minimum insert size for valid paired-end alignments\",\n },\n {\n name: bowtie_maxins_PE,\n prefix: -X,\n type: numeric,\n value: 250,\n min: 0,\n max: NA,\n step: 1,\n label: \"The maximum insert size for valid paired-end alignments\",\n },\n {\n name: bowtie_orientation_PE,\n type: radio,\n choices:\n [\n Not stranded: \"\",\n Forward Reverse: --fr,\n Reverse Forward: --rf,\n Forward Forward: --ff\n ],\n value: \"\",\n label: \"The upstream\/downstream mate orientations for a valid paired-end alignment against the forward reference strand.\",\n },\n {\n name: bowtie_mult_align_limit,\n prefix: -m,\n type: numeric,\n value: 1,\n min: 1,\n max: 10,\n step: 1,\n label: \"Suppress all alignments for a particular read or pair if more than 'x' reportable alignments exist for it\",\n },\n {\n name: bowtie_best,\n prefix: ,\n type: checkbox,\n value: TRUE,\n label: \"--best : Make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum (i.e. number of mismatches, or mismatches in the seed in the case of -n mode) and in terms of the quality values at the mismatched position(s).\",\n },\n {\n name: bowtie_strata,\n prefix: ,\n type: checkbox,\n value: TRUE,\n label: \"--strata : If many valid alignments exist and are reportable (e.g. are not disallowed via the -k option) and they fall into more than one alignment 'stratum', report only those alignments that fall into the best stratum. When --strata is specified, --best must also be specified.\",\n }\n ]\n },\n {\n name: bowtie_SE,\n cname: \"Bowtie SE\",\n command: bowtie,\n category: \"mapping\",\n output_dir: bowtie\/SE,\n inputs: [{ name: read, type: \"reads\" }, { name: index, type: \"bowtie_index\", file: index, description: \"Index files for bowtie alignment\" }],\n outputs: [{ name: bam, type: \"bams\", file: \"{sample}.bam\", description: \"Alignment files\" }],\n options:\n [\n {\n name: bowtie_threads,\n prefix: --threads,\n type: numeric,\n value: 4,\n min: 1,\n max: NA,\n step: 1,\n label: \"Number of threads to use to align reads\",\n },\n {\n name: bowtie_mult_align_limit,\n prefix: -m,\n type: numeric,\n value: 1,\n min: 1,\n max: 10,\n step: 1,\n label: \"Suppress all alignments for a particular read or pair if more than 'x' reportable alignments exist for it\",\n },\n {\n name: bowtie_best,\n prefix: ,\n type: checkbox,\n value: TRUE,\n label: \"--best : Make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum (i.e. number of mismatches, or mismatches in the seed in the case of -n mode) and in terms of the quality values at the mismatched position(s).\",\n },\n {\n name: bowtie_strata,\n prefix: ,\n type: checkbox,\n value: TRUE,\n label: \"--strata : If many valid alignments exist and are reportable (e.g. are not disallowed via the -k option) and they fall into more than one alignment 'stratum', report only those alignments that fall into the best stratum. When --strata is specified, --best must also be specified.\",\n }\n ]\n }\n ],\n install: {\n # bowtie: [\n # \"wget -O bowtie-1.3.0-linux-x86_64.zip https:\/\/sourceforge.net\/projects\/bowtie-bio\/files\/bowtie\/1.3.0\/bowtie-1.3.0-linux-x86_64.zip\/download\",\n # \"unzip bowtie-1.3.0-linux-x86_64.zip\",\n # \"cp bowtie-1.3.0-linux-x86_64\/bowtie* \/usr\/bin\",\n # \"rm -rf bowtie-1.3.0*\"\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 bowtie: [\n \"Langmead, B., Trapnell, C., Pop, M. et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25 (2009). https:\/\/doi.org\/10.1186\/gb-2009-10-3-r25\"\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}" } ]