An Overview of the Phusion Assembler Stages
| Stage | Brief description |
| Data Preparation | Contamination screening, vector and quality clipping. |
| Phusion Read Grouping | Reads that share low copy number words are grouped together into clusters that can be assembled independently of each other. |
| RPphrap | Each cluster of reads, and their associated read pairs, is assembled with PHRAP in an iterative way that allows for contigs to be extended and broken using read pair information. |
| RPjoin | Joins together contigs based on shared reads and sequence overlap as indicated by read pair information. |
| RPono | Scaffolding of contigs based on read pair information. |
| Contamination Screen | Contig and scaffold rejection based on an imbalance of read template origins. |