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https://github.com/ncbi/sra-human-scrubber has the default behavior of replacing identified human reads with poly-"N" strings of equivalent length. Would you be interested in adding this to Deacon?
I imagine this would have follow-up questions regarding paired reads where one read identifies as human while the other read does not. I think that the current behavior discards the pair entirely if at least one read of the pair identifies as human, which makes sense for deletion of human reads.
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enhancementNew feature or requestNew feature or request