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Old 03-01-2015, 01:06 PM   #4
Location: Philadelphia

Join Date: Dec 2012
Posts: 15

We use DeconSeq for human contamination removal. It has an online application as well as a stand-alone version so you can try it out online before spending the time installing it. Unfortunately it looks like their servers are having troubles so you might have a hard time getting to use the online application.

It outputs a fastq with your clean sequences and one with the contaminated seqs. It's definitely worth checking out.
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