[ { "id": "hisat2", "name": "Hisat2", "article": "Kim, D., Paggi, J.M., Park, C. et al. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol 37, 907-915 (2019).", "website": "http:\/\/daehwankimlab.github.io\/hisat2\/", "git": "http:\/\/daehwankimlab.github.io\/hisat2\/", "description": "a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA)", "version": "2.2.1", "documentation": "http:\/\/daehwankimlab.github.io\/hisat2\/manual\/", "multiqc": "hisat2", "commands": [ { "name": "hisat2_PE", "cname": "hisat2 PE", "command": "hisat2", "category": "mapping", "output_dir": "hisat2\/PE", "inputs": [ { "name": "read", "type": "reads" }, { "name": "read2", "type": "reads" }, { "name": "index", "type": "hisat2_index", "file": "index", "description": "Index files for hisat2 alignment" } ], "outputs": [ { "name": "bam", "type": "bams", "file": "{sample}.bam", "description": "Alignment files" } ], "options": [ { "name": "hisat2_reads_type", "type": "radio", "choices": [ { "genome": "genome" }, { "transcriptome": "transcriptome" } ], "value": "transcriptome", "label": "Type of reads sequences" }, { "name": "hisat2_threads", "prefix": "--threads", "type": "numeric", "value": 4, "min": 1, "max": "NA", "step": 1, "label": "Number of threads to use to align reads" }, { "name": "templatelen_adjustment", "prefix": "--no-templatelen-adjustment", "type": "checkbox", "value": true, "label": "Disables template length adjustment for RNA-seq reads" }, { "name": "hisat2_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": "hisat2_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": "hisat2_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": "hisat2_SE", "cname": "hisat2 SE", "command": "hisat2", "category": "mapping", "output_dir": "hisat2\/SE", "inputs": [ { "name": "read", "type": "reads" }, { "name": "index", "type": "hisat2_index", "file": "index", "description": "Index files for hisat2 alignment" } ], "outputs": [ { "name": "bam", "type": "bams", "file": "{sample}.bam", "description": "Alignment files" } ], "options": [ { "name": "hisat2_threads", "prefix": "--threads", "type": "numeric", "value": 4, "min": 1, "max": "NA", "step": 1, "label": "Number of threads to use to align reads" } ] } ], "install": [], "citations": { "hisat2": [ "Kim, D., Paggi, J.M., Park, C. et al. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol 37, 907-915 (2019)" ], "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: hisat2,\n name: Hisat2,\n article: \"Kim, D., Paggi, J.M., Park, C. et al. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol 37, 907-915 (2019).\",\n website: \"http:\/\/daehwankimlab.github.io\/hisat2\/\",\n git: \"http:\/\/daehwankimlab.github.io\/hisat2\/\",\n description: \"a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA)\",\n version: \"2.2.1\",\n documentation: \"http:\/\/daehwankimlab.github.io\/hisat2\/manual\/\",\n multiqc: \"hisat2\",\n commands:\n [\n {\n name: hisat2_PE,\n cname: \"hisat2 PE\",\n command: hisat2,\n category: \"mapping\",\n output_dir: hisat2\/PE,\n inputs: [{ name: read, type: \"reads\" }, { name: read2, type: \"reads\" }, { name: index, type: \"hisat2_index\", file: index, description: \"Index files for hisat2 alignment\" }],\n outputs: [{ name: bam, type: \"bams\", file: \"{sample}.bam\", description: \"Alignment files\" }],\n options:\n [\n {\n name: hisat2_reads_type,\n type: radio,\n choices:\n [\n genome: \"genome\",\n transcriptome: \"transcriptome\",\n ],\n value: \"transcriptome\",\n label: \"Type of reads sequences\",\n },\n {\n name: hisat2_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: templatelen_adjustment,\n prefix: --no-templatelen-adjustment,\n type: \"checkbox\",\n value: TRUE,\n label: \"Disables template length adjustment for RNA-seq reads\",\n },\n {\n name: hisat2_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: hisat2_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: hisat2_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 },\n {\n name: hisat2_SE,\n cname: \"hisat2 SE\",\n command: hisat2,\n category: \"mapping\",\n output_dir: hisat2\/SE,\n inputs: [{ name: read, type: \"reads\" }, { name: index, type: \"hisat2_index\", file: index, description: \"Index files for hisat2 alignment\" }],\n outputs: [{ name: bam, type: \"bams\", file: \"{sample}.bam\", description: \"Alignment files\" }],\n options:\n [\n {\n name: hisat2_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 }\n ],\n install: {\n # hisat2: [\n # \"cd \/tmp\",\n # \"wget -O hisat2-2.2.1-linux-x86_64.zip https:\/\/cloud.biohpc.swmed.edu\/index.php\/s\/oTtGWbWjaxsQ2Ho\/download\",\n # \"unzip hisat2-2.2.1-linux-x86_64.zip\",\n # \"mv hisat2-2.2.1 \/opt\/biotools\/\",\n # \"rm -rf hisat2-2.2.1*\",\n # \"ENV PATH \/opt\/biotools\/hisat2-2.2.1:$PATH \",\n # \"echo \\\"export PATH=$PATH:\/opt\/biotools\/hisat2-2.2.1\\\" >> \/etc\/environment\"\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 hisat2: [\n \"Kim, D., Paggi, J.M., Park, C. et al. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol 37, 907-915 (2019)\"\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}" } ]