Below is a list of the relevant book chapters and articles for each course week.
Course Week 1 - Intro, basic molecular biology & sequence comparison
Chapter 1, page 60
Chapter 6, pages 330-333 [325-328]
Course Week 2 - Introduction to high-throughput sequencing and its applications
Chapter 3, pages 171-173
Chapter 9, page 520
Course Week 3 - Sequence comparison and alignment
Chapter 5, pages 224-231
Course Week 4 - Sequence alignment by dynamic programming
Chapter 5, pages 231-271
Course Week 5 - Optimal alignments in linear space + Scoring matrices
Chapter 5, pages 271-279 and 288-290
Course Week 6 - Heuristic database searches with protein sequences
Chapter 9, pages 510-511
Course Week 7 - Heuristic database searches with nucleotide sequences
BLAT article by Kent
Course Week 8 - Mapping using suffix tries, trees, and arrays, Burrows-Wheeler-transform and FM-index
Chapter 9, pages 468-528
Course Week 9 - Genome sequence assembly
Chapter 3, pages 116-170
Articles by Simpson & Pop and by Mathé et al.
Course Week 10 - Clustering
Chapter 8, pages 416-462
Course Week 11 - Multiple sequence alignment
Chapter 5, pages 280-285 and 293-294
Course Week 12 - Phylogenetic reconstruction
Chapter 7, pages 352-400
Course Week 13 - Motif discovery
Chapter 2, pages 66-105, 113-115
Course Week 14 - Searching with sequence profiles and hidden Markov models
Chapter 10, pages 530-569
HMM article by Eddy
Course Week 15 - Gene prediction
Chapter 11, pages 626-627
Gene prediction article by Mathé et al.