Guppy will sort reads into "pass" and "fail" folders by default, where reads in the "pass" folder have a mean Q-score above a particular threshold, but can be disabled with the `--disable_qscore_filtering` flag. The`--min_qscore` flag can be used to set your own Q-score pass/fail threshold.

The default value for this is 8 for DNA fast models, 9 for DNA hac models, 10 for DNA sup models, and 7 for all RNA models.

Please see the “Setting up a run: configurations and parameters” section in the Guppy protocol for more details and a full listing of available options.