Table 3.

Four combinations of schemes between two base-calling and two quality scoring methods

		Quality scoring
		L1-regularized logistic regression	Lookup table strategy
Base-calling	Bustard	Bustard+Logistic	Bustard+Lookup
	3Dec	3Dec+Logistic	3Dec+Lookup

We have two base calling methods: Bustard, the default method embedded in the Illumina sequencers; 3Dec, our newly developed method. We also have two quality scoring methods: Lookup, the lookup table strategy adopted by Illumina; Logistic, the L ₁-regularized logistic regression model proposed in this study