The course's main text book is "Biological Sequence Analysis" by Durbin et al.
The course is roughly divided among the following topics:
Intro to molecular biology
Sequence alignment (DP, Needleman-Wunch)
Distributions and p-values
Sequencing technologies, differential expression analysis
Suffix trees
BWA
Multiple alignment
Markov models and HMMs
Viterbi algorithm
MLE, for example: inference of phylogenetic trees
EM
mHG and enrichment, PPI
Summary, applications and new directions