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Systematic base-calling biases in Illumina exist. I.e. read one thing going one way, something else going the other.
How does Seqprep do error correction?
Quality scores Q_i = -10 * log_10(P(i is wrong)) Given that base Xi is x:
= -10 * log_10(1-P(Y=x|Xi=x))
Quality of an alignment: Q1 (quality of read 1), Q2 (quality of read 2), Qa (alignment quality).
If we assume that the alignment is perfect: