{"type":"doc","content":[{"type":"extension","attrs":{"layout":"default","extensionType":"com.atlassian.confluence.macro.core","extensionKey":"toc","parameters":{"macroParams":{"minLevel":{"value":"1"},"maxLevel":{"value":"7"},"type":{"value":"flat"},"separator":{"value":"pipe"}},"macroMetadata":{"macroId":{"value":"84eab535d6596e1b7375564f6b694a3d"},"schemaVersion":{"value":"1"},"title":"Table of Contents"}},"localId":"5831c522-1109-43f9-9b3e-4deaf84bdfff"}},{"type":"heading","attrs":{"level":2},"content":[{"text":"Overview","type":"text"}]},{"type":"paragraph","content":[{"text":"Trimmomatic","type":"text","marks":[{"type":"link","attrs":{"href":"http://www.usadellab.org/cms/?page=trimmomatic"}}]},{"text":" is a flexible read trimming tool for Illumina NGS data.","type":"text"}]},{"type":"heading","attrs":{"level":2},"content":[{"text":"Using","type":"text"}]},{"type":"paragraph","content":[{"text":"Use the module name ","type":"text"},{"text":"trimmomatic","type":"text","marks":[{"type":"code"}]},{"text":" to discover versions available and to load the application.","type":"text"}]},{"type":"paragraph","content":[{"text":"ARCC has created a wrapper script to make using the commands easier so you simply need to use the ","type":"text"},{"text":"trimmomatic","type":"text","marks":[{"type":"code"}]},{"text":" call from the command-line:","type":"text"}]},{"type":"codeBlock","content":[{"text":"[]$ trimmomatic\nUsage:\n PE [-version] [-threads ] [-phred33|-phred64] [-trimlog ] [-summary ] [-quiet] [-validatePairs] [-basein | ] [-baseout | ] ...\n or:\n SE [-version] [-threads ] [-phred33|-phred64] [-trimlog ] [-summary ] [-quiet] ...\n or:\n -version\n\n[]$ trimmomatic PE -version\n0.39 ","type":"text"}]},{"type":"heading","attrs":{"level":4},"content":[{"text":"Multicore:","type":"text"}]},{"type":"paragraph","content":[{"text":"The ","type":"text"},{"text":"trimmomatic","type":"text","marks":[{"type":"code"}]},{"text":" command can be ran with multiple threads. Run the ","type":"text"},{"text":"trimmomatic","type":"text","marks":[{"type":"code"}]},{"text":" call from the command-line to see details on the ","type":"text"},{"text":"-threads","type":"text","marks":[{"type":"code"}]},{"text":" option.","type":"text"}]},{"type":"paragraph","content":[{"text":"Example:","type":"text","marks":[{"type":"strong"}]}]},{"type":"codeBlock","content":[{"text":"[]$ salloc -A arcc -t 1:00:00 -c 16\n\n[@m001 trimmmomatic] trimmomatic PE -threads 16 \\\n data/SRR2589044_1.fastq.gz data/SRR2589044_2.fastq.gz \\\n SRR2589044_1.trim.fastq.gz SRR2589044_1un.trim.fastq.gz \\\n SRR2589044_2.trim.fastq.gz SRR2589044_2un.trim.fastq.gz \\\n SLIDINGWINDOW:4:20 MINLEN:25 ILLUMINACLIP:adapters/NexteraPE-PE.fa:2:40:15","type":"text"}]},{"type":"heading","attrs":{"level":3},"content":[{"text":"Adapters:","type":"text"}]},{"type":"paragraph","content":[{"text":"Adapters are available at the ","type":"text"},{"text":"trimmomatic Git Hub","type":"text","marks":[{"type":"link","attrs":{"href":"https://github.com/usadellab/Trimmomatic"}}]},{"text":". ","type":"text"}]},{"type":"paragraph","content":[{"text":"On ","type":"text"},{"text":"Beartooth","type":"text","marks":[{"type":"strong"}]},{"text":" and ","type":"text"},{"text":"medicineBow","type":"text","marks":[{"type":"strong"}]},{"text":", the following adapters are available, and can be copied from: ","type":"text"},{"text":"/apps/u/opt/linux/trimmomatic/0.39/adapters/","type":"text","marks":[{"type":"code"}]}]},{"type":"codeBlock","content":[{"text":"NexteraPE-PE.fa TruSeq2-PE.fa TruSeq2-SE.fa TruSeq3-PE-2.fa TruSeq3-PE.fa TruSeq3-SE.fa","type":"text"}]},{"type":"paragraph"}],"version":1}

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