How to use ./Antibiotic_resistanse.sh [-cut bases off the start if quality below] [-cut bases off the end if quality below] [-% of non-reference bases] or ./Antibiotic_resistanse_mac.sh [-cut bases off the start if quality below] [-cut bases off the end if quality below] [-% of non-reference bases] [path to .jar trimmomatic] [path to .jar VarSacn]
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