Intro and clear concept about de bruijn Graphs

1. de Bruijn graphs

2. De Bruijn graph is a
directed graph
representing overlaps
between sequences of
symbols
What are de Bruijn graphs ?

3. History
Massiveness of the province
Restricted sources of communication
Language difference
Need of the time
Progress of locals
 De bruijn was a person who invented these graphs
 He was interested in purely abstract problems.
 He tried to solve so-called universal string problem.
 Universal string problem :
Finding a circular or graphical string containing each binary k-mer
exactly once.

4. Types of De Bruijn Graphs
 Eulerian Path
 Hamiltonian Trail

5. Information
3 Steps
De Bruijn
Graph
Directed
graph

6. INPUT/OUTPUT
Input :
A set of k-mers patterns.
Output :
De Bruijn graphs

7. K-mers
 All the possible subsequences (of
length k) from a read obtained
through DNA Sequencing
Small chunks 001 110
000 101
001110000101

8. INPUT
Whole Sequence :
If whole sequence is given we have to divide it into k-
mers
K-mers

9. 1st Step
The first step is to choose a k-mer size, and split the
original sequence into its k-mer components( if sequence
is given)

11. Whole sequence
T A A T G C C A T G G G A TAA
ATG
ATG
CAT
CCA
GCC
TGC
AAT
TGG
GGG
GGA

12. Create Nodes.
Build edges.
Create directions.
Construction of graph

14. Nodes
 We consider each k-mer as edge.
 2 nodes for each edge
TAA
? ?

15. Nodes
 First :
Prefix of edge
 Second :
Suffix of edge
TAA
TA AA
N-1

16. K-mers
TAA
ATG
ATG
CAT
CCA
GCC
TGC
AAT
TGG
GGG
GGA
T A A T G C C A T G G G A

17. TAA
TA AA
TGC
TG GC
ATG
AT TG
AAT
AA AT
Highlight the similar nodes closer

18. TAA
TA AA
TGC
TG GC
ATG
AT TG
Make the similar nodes closer

19. TAA
TA AA
TGC
TG GC
ATG
AT TG
Glue the similar nodes

20. TAA
TA AA
TGC
TG GC
ATG
AT TG
AAT
Glue the similar nodes

21. 2nd Step
Then a directed graph is constructed by connecting pairs
of k-mers with overlaps between the first k-1
nucleotides and the last k-1 nucleotides

22. For All K-mers

23. Glue the similar nodes again.

34.  Use whole sequence of first edge
 The Only Use the last alphabet from the
intermediate edges.
 Build the genome.
Construction of Genome

35. T A A T G C C A
T G G G A

36. De bruijn graph and genome
assembly
 Genome assembly:
 It simply the genome sequence produced after chromosomes have been
fragmented, those fragments have been sequenced, and the resulting
sequences have been put back together.

37. De bruijn graph and NGS
 Mostly used for Sanger reads
 NGS instruments rapidly and inexpensively decode the sequences of millions of
small fragments
 Read size remained short
 With shorter reads, it was more common to find spurious overlaps between read
pairs.

38.  Short
 Shorter
 Collectively characterists of genome lost

39. De bruijn graph based genome
assembly algorithm

40. Drawbacks
 De Bruijn graphs do not preserve positional information.
 . Longer the read size, more one has to lose.

42. Any Question?