[ { "id": "accel_align", "name": "Accel-align is a fast alignment tool implemented in C++", "article": "10.1186\/s12859-021-04162-z", "website": "https:\/\/github.com\/raja-appuswamy\/accel-align-release", "git": "https:\/\/github.com\/raja-appuswamy\/accel-align-release", "description": "a fast sequence mapper and aligner based on the seed-embed-extend method", "version": "2.0", "documentation": "https:\/\/github.com\/raja-appuswamy\/accel-align-release", "multiqc": "custom", "commands": [ { "name": "accel_align_PE", "cname": "Accel-align PE", "command": "accalign-x86-64", "category": "mapping", "output_dir": "accel_align\/PE", "inputs": [ { "name": "read", "type": "reads" }, { "name": "read2", "type": "reads" }, { "name": "index", "type": "accel_align_index", "file": "index", "description": "Index files for accel_align alignment" } ], "outputs": [ { "name": "bam", "type": "bams", "file": "{sample}.bam", "description": "Alignment files" } ], "options": [ { "name": "accel_align_threads", "prefix": "-t", "type": "numeric", "value": 4, "min": 1, "max": "NA", "step": 1, "label": "Number of threads to use" }, { "name": "accel_align_seed_length", "prefix": "-l", "type": "numeric", "value": 32, "min": 10, "max": 100, "step": 1, "label": "length of seed" }, { "name": "accel_align_insert_size", "prefix": "-p", "type": "numeric", "value": 1000, "min": 10, "max": 4000, "step": 10, "label": "the maximum distance allowed between the paired-end reads (maximum read length supported are 512)" }, { "name": "accel_align_softclipping", "prefix": "-s", "type": "checkbox", "value": false, "label": "Take into account softclipping" }, { "name": "accel_align_alignment_free", "prefix": "-x", "type": "checkbox", "value": false, "label": "alignment-free mapping mode where the position is reported without the CIGAR string" } ] }, { "name": "accel_align_SE", "cname": "Accel-align SE", "command": "accalign-x86-64", "category": "mapping", "output_dir": "accel_align\/SE", "inputs": [ { "name": "read", "type": "reads" }, { "name": "index", "type": "accel_align_index", "file": "index", "description": "Index files for accel_align alignment" } ], "outputs": [ { "name": "bam", "type": "bams", "file": "{sample}.bam", "description": "Alignment files" } ], "options": [ { "name": "accel_align_threads", "prefix": "-t", "type": "numeric", "value": 4, "min": 1, "max": "NA", "step": 1, "label": "Number of threads to use" }, { "name": "accel_align_seed_length", "prefix": "-l", "type": "numeric", "value": 32, "min": 10, "max": 100, "step": 1, "label": "length of seed" }, { "name": "accel_align_softclipping", "prefix": "-s", "type": "checkbox", "value": false, "label": "Take into account softclipping" }, { "name": "accel_align_alignment_free", "prefix": "-x", "type": "checkbox", "value": false, "label": "alignment-free mapping mode where the position is reported without the CIGAR string" } ] } ], "install": { "accel_align": [ "cd \/opt\/biotools", "git clone https:\/\/github.com\/raja-appuswamy\/accel-align-release.git", "ENV PATH \/opt\/biotools\/accel-align-release:$PATH" ], "Intel_TBB": [ "apt-get install -y libtbb-dev" ], "samtools": [ "cd \/opt\/biotools", "wget https:\/\/github.com\/samtools\/samtools\/releases\/download\/1.9\/samtools-1.9.tar.bz2", "tar -xvjf samtools-1.9.tar.bz2", "cd samtools-1.9", ".\/configure && make", "cd ..", "mv samtools-1.9\/samtools bin\/samtools", "rm -r samtools-1.9 samtools-1.9.tar.bz2" ] }, "citations": { "accel_align": [ "Yan, Y., Chaturvedi, N. & Appuswamy, R. Accel-Align: a fast sequence mapper and aligner based on the seed-embed-extend method. BMC Bioinformatics 22, 257 (2021)." ], "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: accel_align,\n name: Accel-align is a fast alignment tool implemented in C++,\n article: 10.1186\/s12859-021-04162-z,\n website: \"https:\/\/github.com\/raja-appuswamy\/accel-align-release\",\n git: \"https:\/\/github.com\/raja-appuswamy\/accel-align-release\",\n description: \"a fast sequence mapper and aligner based on the seed-embed-extend method\",\n version: \"2.0\",\n documentation: \"https:\/\/github.com\/raja-appuswamy\/accel-align-release\",\n multiqc: \"custom\",\n commands:\n [\n {\n name: accel_align_PE,\n cname: \"Accel-align PE\",\n command: accalign-x86-64,\n category: \"mapping\",\n output_dir: accel_align\/PE,\n inputs: [{ name: read, type: \"reads\" }, { name: read2, type: \"reads\" }, { name: index, type: \"accel_align_index\", file: index, description: \"Index files for accel_align alignment\" }],\n outputs: [{ name: bam, type: \"bams\", file: \"{sample}.bam\", description: \"Alignment files\" }],\n options:\n [\n {\n name: accel_align_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: accel_align_seed_length,\n prefix: -l,\n type: numeric,\n value: 32,\n min: 10,\n max: 100,\n step: 1,\n label: \"length of seed\",\n },\n {\n name: accel_align_insert_size,\n prefix: -p,\n type: numeric,\n value: 1000,\n min: 10,\n max: 4000,\n step: 10,\n label: \"the maximum distance allowed between the paired-end reads (maximum read length supported are 512)\",\n },\n {\n name: accel_align_softclipping,\n prefix: -s,\n type: checkbox,\n value: FALSE,\n label: \"Take into account softclipping\",\n },\n {\n name: accel_align_alignment_free,\n prefix: -x,\n type: checkbox,\n value: FALSE,\n label: \"alignment-free mapping mode where the position is reported without the CIGAR string\",\n }\n ]\n },\n {\n name: accel_align_SE,\n cname: \"Accel-align SE\",\n command: accalign-x86-64 ,\n category: \"mapping\",\n output_dir: accel_align\/SE,\n inputs: [{ name: read, type: \"reads\" }, { name: index, type: \"accel_align_index\", file: index, description: \"Index files for accel_align alignment\" }],\n outputs: [{ name: bam, type: \"bams\", file: \"{sample}.bam\", description: \"Alignment files\" }],\n options:\n [\n {\n name: accel_align_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: accel_align_seed_length,\n prefix: -l,\n type: numeric,\n value: 32,\n min: 10,\n max: 100,\n step: 1,\n label: \"length of seed\",\n },\n {\n name: accel_align_softclipping,\n prefix: -s,\n type: checkbox,\n value: FALSE,\n label: \"Take into account softclipping\",\n },\n {\n name: accel_align_alignment_free,\n prefix: -x,\n type: checkbox,\n value: FALSE,\n label: \"alignment-free mapping mode where the position is reported without the CIGAR string\",\n }\n ]\n }\n ],\n install: {\n accel_align: [\n \"cd \/opt\/biotools\",\n \"git clone https:\/\/github.com\/raja-appuswamy\/accel-align-release.git\",\n \"ENV PATH \/opt\/biotools\/accel-align-release:$PATH\",\n ],\n Intel_TBB: [\n \"apt-get install -y libtbb-dev\",\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 accel_align: [\n \"Yan, Y., Chaturvedi, N. & Appuswamy, R. Accel-Align: a fast sequence mapper and aligner based on the seed-embed-extend method. BMC Bioinformatics 22, 257 (2021).\"\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}" } ]