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short Read/percentage threshold for bacterium presence in metagenome

Given that you're already using kraken2, I recommend bracken: https://github.com/jenniferlu717/Bracken Bracken is a companion program to Kraken 1, KrakenUniq, or Kraken 2 While Kraken classifies ...
gringer's user avatar
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short Read/percentage threshold for bacterium presence in metagenome

Thats an interesting question. I do this stuff all the time and don't have a fixed cut-off. What I am certain about is 100 is marginal evidence of a species. So I personally would be reluctant to ...
M__'s user avatar
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