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Old 02-01-2015, 05:29 PM   #2
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

I have never heard of bmtagger, but at JGI we use this pipeline for human contaminant removal. It's quite thorough, and carefully designed to have zero false-positive removals when processing any domain other than animal. The output is two fastq files, one with the human reads and one with the clean reads, and it keeps pairs together.
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