De bruijn graphs
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De Bruijn graphs are directed graphs used to represent overlaps between sequences of symbols. They are constructed by splitting a DNA sequence into k-mers (subsequences of length k), creating nodes for each k-mer, and connecting nodes with edges where the k-mers overlap by k-1 nucleotides. De Bruijn graphs are commonly used for genome assembly from next-generation sequencing data by reconstructing the original sequence from the k-mers. They allow mapping short reads onto a reference genome despite the reads being shorter than the repeats within the genome.
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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
- 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?