04_Genome_Assembly

Genome Assembly

De novo genome assembly using De Bruijn graph algorithms.

Topics Covered

• De Bruijn Graphs: Graph-based representation of sequencing reads
• K-mers: Sequence fragmentation and overlap detection
• Contig Assembly: Building contiguous sequences from short reads

Files

File	Description
de_bruijn_assembly.ipynb	Main assembly notebook
data/	Input sequencing reads and outputs

Key Concepts

The De Bruijn graph approach:

1. Fragment reads into k-mers
2. Build a graph where nodes are (k-1)-mers
3. Edges represent k-mers connecting nodes
4. Find Eulerian paths to reconstruct sequences