An overview of the workflow and algorithms of SAVAGE. (A) The three stages of SAVAGE. Each assembles sequences into longer sequences. For clarity, we assign different names to the sequences output by each stage: contigs, maximally extended contigs, and master contigs, respectively. (B) Principle of overlap graph construction and distinction among the reads between errors and shared mutations. (C) Each stage has two steps: first, the overlap graph construction; second, assembly. This panel summarizes the differences in each step between the three stages. During overlap graph-based assembly, steps 4 to 6 are repeated iteratively until there are no edges left in the overlap graph.