[ { "id": "snap", "name": "Scalable Nucleotide Alignment Program", "article": "arXiv:1111.5572v1", "website": "https:\/\/www.microsoft.com\/en-us\/research\/project\/snap\/", "git": "https:\/\/github.com\/amplab\/snap", "description": "fast and accurate aligner for short DNA reads. It is optimized for modern read lengths of 100 bases or higher, and align them quickly through a hash-based indexing scheme.", "version": "2.0.3", "documentation": "https:\/\/github.com\/amplab\/snap\/tree\/master\/docs", "multiqc": "custom", "commands": [ { "name": "snap_PE", "cname": "snap PE", "command": "snap-aligner paired", "category": "mapping", "output_dir": "snap\/PE", "inputs": [ { "name": "read", "type": "reads" }, { "name": "read2", "type": "reads" }, { "name": "index", "type": "snap_index", "file": "index", "description": "Index files for snap alignment" } ], "outputs": [ { "name": "bam", "type": "bams", "file": "{sample}.bam", "description": "Alignment file" } ], "options": [ { "name": "snap_threads", "prefix": "-t", "type": "numeric", "value": 4, "min": 1, "max": "NA", "step": 1, "label": "Number of threads to use" }, { "name": "snap_seed_number", "prefix": "-n", "type": "numeric", "value": 4, "min": 1, "max": 10, "step": 1, "label": "number of seeds to use per read" }, { "name": "snap_min_insert_size", "prefix": "-s", "type": "numeric", "value": 0, "min": 10, "max": 400, "step": 10, "label": "minimum spacing to allow between paired ends" }, { "name": "snap_max_insert_size", "prefix": "-s", "type": "numeric", "value": 1000, "min": 10, "max": 3000, "step": 10, "label": "maximum spacing to allow between paired ends" }, { "name": "snap_force_spacing", "prefix": "-sf", "type": "checkbox", "value": false, "label": "force spacing to lie between min and max." }, { "name": "snap_disable_alt_awareness", "prefix": "-A-", "type": "checkbox", "value": false, "label": "Disable ALT awareness. By default snap try to map reads to the primary assembly and only to choose ALT alignments when they're much better, and to compute MAPQ for non-ALT alignments using only non-ALT hits. This flag disables that behavior" }, { "name": "snap_max_score_gap", "prefix": "-asg", "type": "numeric", "value": 2, "min": 1, "max": 10, "step": 1, "label": "Maximum score gap to prefer a non-ALT alignment. If the best non-ALT alignment is more than this much worse than the best ALT alignment emit the ALT alignment as the primary result rather than as" } ] }, { "name": "snap_SE", "cname": "snap SE", "command": "snap-aligner single", "category": "mapping", "output_dir": "snap\/SE", "inputs": [ { "name": "read", "type": "reads" }, { "name": "index", "type": "snap_index", "file": "index", "description": "Index files for snap alignment" } ], "outputs": [ { "name": "bam", "type": "bams", "file": "{sample}.bam", "description": "Alignment file" } ], "options": [ { "name": "snap_threads", "prefix": "-t", "type": "numeric", "value": 4, "min": 1, "max": "NA", "step": 1, "label": "Number of threads to use" }, { "name": "snap_seed_number", "prefix": "-n", "type": "numeric", "value": 4, "min": 1, "max": 10, "step": 1, "label": "number of seeds to use per read" }, { "name": "snap_disable_alt_awareness", "prefix": "-A-", "type": "checkbox", "value": false, "label": "Disable ALT awareness. By default snap try to map reads to the primary assembly and only to choose ALT alignments when they're much better, and to compute MAPQ for non-ALT alignments using only non-ALT hits. This flag disables that behavior" }, { "name": "snap_max_score_gap", "prefix": "-asg", "type": "numeric", "value": 2, "min": 1, "max": 10, "step": 1, "label": "Maximum score gap to prefer a non-ALT alignment. If the best non-ALT alignment is more than this much worse than the best ALT alignment emit the ALT alignment as the primary result rather than as" } ] } ], "install": [], "citations": { "snap": [ "Faster and More Accurate Sequence Alignment with SNAP. Matei Zaharia, William J. Bolosky, Kristal Curtis, Armando Fox, David Patterson, Scott Shenker, Ion Stoica, Richard M. Karp, and Taylor Sittler. arXiv:1111.5572v1, November 2011." ] }, "yaml": "{\n id: snap,\n name: Scalable Nucleotide Alignment Program,\n article: \"arXiv:1111.5572v1\",\n website: \"https:\/\/www.microsoft.com\/en-us\/research\/project\/snap\/\",\n git: \"https:\/\/github.com\/amplab\/snap\",\n description: \"fast and accurate aligner for short DNA reads. It is optimized for modern read lengths of 100 bases or higher, and align them quickly through a hash-based indexing scheme.\",\n version: \"2.0.3\",\n documentation: \"https:\/\/github.com\/amplab\/snap\/tree\/master\/docs\",\n multiqc: \"custom\",\n commands:\n [\n {\n name: snap_PE,\n cname: \"snap PE\",\n command: snap-aligner paired,\n category: \"mapping\",\n output_dir: snap\/PE,\n inputs: [{ name: read, type: \"reads\" }, { name: read2, type: \"reads\" }, { name: index, type: \"snap_index\", file: index, description: \"Index files for snap alignment\" }],\n outputs: [{ name: bam, type: \"bams\", file: \"{sample}.bam\", description: \"Alignment file\" }],\n options:\n [\n {\n name: snap_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: snap_seed_number,\n prefix: -n,\n type: numeric,\n value: 4,\n min: 1,\n max: 10,\n step: 1,\n label: \"number of seeds to use per read\",\n },\n {\n name: snap_min_insert_size,\n prefix: -s,\n type: numeric,\n value: 0,\n min: 10,\n max: 400,\n step: 10,\n label: \"minimum spacing to allow between paired ends\",\n },\n {\n name: snap_max_insert_size,\n prefix: -s,\n type: numeric,\n value: 1000,\n min: 10,\n max: 3000,\n step: 10,\n label: \"maximum spacing to allow between paired ends\",\n },\n {\n name: snap_force_spacing,\n prefix: -sf,\n type: checkbox,\n value: FALSE,\n label: \"force spacing to lie between min and max.\",\n },\n {\n name: snap_disable_alt_awareness,\n prefix: -A-,\n type: checkbox,\n value: FALSE,\n label: \"Disable ALT awareness. By default snap try to map reads to the primary assembly and only to choose ALT alignments when they're much better, and to compute MAPQ for non-ALT alignments using only non-ALT hits. This flag disables that behavior\",\n },\n { \n name: snap_max_score_gap,\n prefix: -asg,\n type: numeric,\n value: 2,\n min: 1,\n max: 10,\n step: 1,\n label: \"Maximum score gap to prefer a non-ALT alignment. If the best non-ALT alignment is more than this much worse than the best ALT alignment emit the ALT alignment as the primary result rather than as\",\n },\n ]\n },\n {\n name: snap_SE,\n cname: \"snap SE\",\n command: snap-aligner single,\n category: \"mapping\",\n output_dir: snap\/SE,\n inputs: [{ name: read, type: \"reads\" }, { name: index, type: \"snap_index\", file: index, description: \"Index files for snap alignment\" }],\n outputs: [{ name: bam, type: \"bams\", file: \"{sample}.bam\", description: \"Alignment file\" }],\n options:\n [\n {\n name: snap_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: snap_seed_number,\n prefix: -n,\n type: numeric,\n value: 4,\n min: 1,\n max: 10,\n step: 1,\n label: \"number of seeds to use per read\",\n },\n {\n name: snap_disable_alt_awareness,\n prefix: -A-,\n type: checkbox,\n value: FALSE,\n label: \"Disable ALT awareness. By default snap try to map reads to the primary assembly and only to choose ALT alignments when they're much better, and to compute MAPQ for non-ALT alignments using only non-ALT hits. This flag disables that behavior\",\n },\n { \n name: snap_max_score_gap,\n prefix: -asg,\n type: numeric,\n value: 2,\n min: 1,\n max: 10,\n step: 1,\n label: \"Maximum score gap to prefer a non-ALT alignment. If the best non-ALT alignment is more than this much worse than the best ALT alignment emit the ALT alignment as the primary result rather than as\",\n },\n ]\n }\n ],\n install: {\n # snap: [\n # \"cd \/opt\/biotools\",\n # \"git clone https:\/\/github.com\/amplab\/snap.git\",\n # \"cd snap\",\n # \"make -j 8\",\n # \"ENV PATH \/opt\/biotools\/snap:$PATH\",\n # ]\n },\n citations: {\n snap: [\n \"Faster and More Accurate Sequence Alignment with SNAP. Matei Zaharia, William J. Bolosky, Kristal Curtis, Armando Fox, David Patterson, Scott Shenker, Ion Stoica, Richard M. Karp, and Taylor Sittler. arXiv:1111.5572v1, November 2011.\"\n ]\n }\n}" } ]