Puzzle Hi-C: An accurate scaffolding software
Fig 1
The Puzzle Hi-C pipeline contains three steps: mapping, scaffolding, and building. Ordering and orientation adopt an iterative method to obtain accurate assemblies via multiple iterations. Puzzle Hi-C introduces a dynamic, triangle window strategy during assembling. The triangle window is initially small but expands with interactions to produce more effective clustering. Finally, the genome is assembled according to the scaffolding results and output in final fasta and apg format files.