Exercise 1 ATGGC for k=3 (ATG, TGG, GGC, GCC, CCT, CTG, TGC, GCA)

GGCCT
K-mer k-1 (Prefix) k-1 (Suffix)
CCTGC for k=2
CTGCA ATG AT TG

Remember this rule: TGG TG GG

GGC GG GC
• Eulerian path – visit every edge (arc)
once GCC GC CC
• Hamiltonian path – visit every node once CCT CC CT

CTG CT TG

TGC TG GC
Which means, this is a Eulerian walk GCA GC CA

CCT
CTG
CT 5 CC
6 GCC
ATG 4
TGC 8
AT TG 7 GC GCA CA Contig: ATGGCCTGCA
1
2 3
TGG GGC
GG
Exercise 2
Build de Bruijn graph(s); make sure to enumerate each edge based on the reads below; what is the
assembled contig? What path would it be in this cas?

Reads: TAA, AAT, ATG, TGT, GTT

Exercise 3
Build de Bruijn graph(s); make sure to enumerate each edge based on the reads below; what is the
assembled contig? What path would it be in this cas?

Reads: ATG, TGC, GCA, CAG, AGC, GCG