SummarySo in summary, the de novo assembly algorithm goes through these stages:
- Make a table of the words seen in the reads.
- Build a de Bruijn graph from the word table.
- Use the reads to resolve the repeats in the graph.
- Use the information from paired reads to resolve larger repeats and perform scaffolding if necessary.
- Output resulting contigs based on the paths, optionally including annotations from the scaffolding step.