KneadData

usage: kneaddata [-h] [--version] [-v] -i INPUT -o OUTPUT_DIR
                 [-db REFERENCE_DB] [--bypass-trim]
                 [--output-prefix OUTPUT_PREFIX] [-t <1>] [-p <1>]
                 [-q {phred33,phred64}] [--run-bmtagger] [--run-trf]
                 [--run-fastqc-start] [--run-fastqc-end] [--store-temp-output]
                 [--remove-intermediate-output] [--cat-final-output]
                 [--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [--log LOG]
                 [--trimmomatic TRIMMOMATIC_PATH] [--max-memory MAX_MEMORY]
                 [--trimmomatic-options TRIMMOMATIC_OPTIONS]
                 [--bowtie2 BOWTIE2_PATH] [--bowtie2-options BOWTIE2_OPTIONS]
                 [--no-discordant] [--cat-pairs] [--reorder] [--serial]
                 [--bmtagger BMTAGGER_PATH] [--trf TRF_PATH] [--match MATCH]
                 [--mismatch MISMATCH] [--delta DELTA] [--pm PM] [--pi PI]
                 [--minscore MINSCORE] [--maxperiod MAXPERIOD]
                 [--fastqc FASTQC_PATH]