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NGSeasy: trimmomatic

trimmomatic [goo.gl/sLDXNH]

DOCKER_RUN="docker run -P -w /home/pipeman -e HOME=/home/pipeman -e USER=pipeman --user pipeman"

    ${DOCKER_RUN} \
    --rm=true \
    -v ${PROJECT_DIR}:/home/pipeman/ngs_projects \
    -v ${NGSResources}:/home/pipeman/ngs_resources \
    --name trimmomatic_${BAM_PREFIX} \
    -t compbio/ngseasy-trimmomatic:${NGSEASYVERSION} java -XX:ParallelGCThreads=1 -jar /usr/local/pipeline/Trimmomatic-0.32/trimmomatic-0.32.jar \
    PE \
    -threads ${NCPU} \
    ${SOUTDocker}/fastq/${FQ1} \
    ${SOUTDocker}/fastq/${FQ2} \
    ${qcPEFQ1} ${qcSEFQ1} \
    ${qcPEFQ2} ${qcSEFQ2} \
    ILLUMINACLIP:${adapter_fa}:2:30:10:5:true \
    LEADING:3 \
    TRAILING:3 \
    SLIDINGWINDOW:4:15 \
    AVGQUAL:2 \
    MINLEN:75
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compbio