====== Seqprep lecture notes ======
Phred:
  * 66 -> 0 (33)  (Or not... makes sense to not have 0)
  * 33 - 64 = -31 in most cases

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 our base call based on an alignment:  Q1 (quality of read 1), Q2 (quality of read 2), Qa (alignment quality).

If we assume that the alignment is perfect:
  * Bases 1 and 2 agree: Q1 + Q2
  * Bases 1 and 2 disagree: Q1 - Q2?