ahmed-zaher / genome-assembler

Genome-Assembler

A basic genome assembler to assemble contigs of a genome from a set of error-prone reads. This project is based on the Genome Assembly Programming Challenge capstone project on Coursera.

The assembler work as follows:

• It breaks given reads into k-mers (with k = 20)
• Build De Bruijn graph from these k-mers
• Remove tips from De Bruijn graph
• Remove bubbles from De Bruijn graph to account for sequencing errors
• Generate contigs of the original genome by finding maximal non-branching paths and isolated cycles in the De Bruijn graph