Fig. 1: AmpliconReconstructor (AR) overview.

a Workflow to produce the necessary inputs for AR. AR accepts OM data in the consensus map (CMAP) format. b High-level overview of the AR method, where the inputs and outputs are shown outside the gray box representing the AR wrapper. The green loop-back arrow on the SegAligner module represents the identification of reference segments not encoded in the breakpoint graph. c A breakpoint graph with N segments. d In silico digestion of breakpoint graph segments (orientation given by +/−) from (c) to produce graph OM segments. e Alignment of graph OM segments to OM contigs produces a scaffold of segment-contig alignments. f AR uses the structure of the breakpoint graph to identify paths between scaffold alignment endpoints which are also paths in the breakpoint graph. AR generates composite optical maps from combined path segments to score each candidate path against the gap in the scaffold. g AR identifies a candidate path with maximum score out of the possible imputed paths between two alignments. h AR links individual scaffolds sharing overlap between graph segments. The resulting graph has two types of edges, allowed (gray) and forbidden (red). i Cumulative precision and recall curves based on simulated OM data for AR using SegAligner, calculated with the Length (bp) LCS metric. Line color indicates the copy number (CN) of the simulated amplicon. Source data are provided as a Source data file.