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Old 08-08-2013, 09:39 AM   #1
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Default Using CASAVA versus cutadapt for adapter trimming

I am getting started with HaloPlex using Illumina platform. They suggest using cutadapt for adapter trimming. However, CASAVA relatively recently added --adapter-sequence option for adapter trimming. If I use CASAVA, I can skip additional step of data processing. Is there any disadvantage to using CASAVA instead of cutadapt?
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