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PanPhlAn profile - strain detection

Strain detection thresholds

Depending on the sample coverage depth and expected species abundance, different sensitivity thresholds for strain presence/absence detection can be chosen. This includes a strain minimum coverage and settings for accepted shapes of strain abundance curves.
--min_coverage 5 --left_max 1.18 --right_min 0.82 (very stringent)
--min_coverage 2 --left_max 1.25 --right_min 0.75 (default)
--min_coverage 1 --left_max 1.70 --right_min 0.30 (very sensitive)

Gene-family detection thresholds

For all samples in which a strain could be detected, we define presence and absence of gene-families based on a threshold on normalized coverage curves:
--th_present 0.5
All gene-families larger than 0.5 are considered as present (1), and lower as absent (0).