HiFi presets

With v2.5.0 we introduced the concept of recommended parameter presets called --hifi-preset.

Preset Definition
SYMMETRIC --ccs --min-score 0 --min-end-score 80 --min-ref-span 0.75 --same --single-end
SYMMETRIC-ADAPTERS --ccs --min-score 0 --min-end-score 80 --min-ref-span 0.75 --same --ignore-missing-adapters --single-end
ASYMMETRIC --ccs --min-score 80 --min-end-score 50 --min-ref-span 0.75 --different --min-scoring-regions 2

For barcoded adapter libraries, SYMMETRIC-ADAPTERS will increase demultiplexed yield. More info under barcoded adapter FAQ

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