Schematic diagrams of the process flow used in Patch.

(A) Gap-filling: a gap (with N’s) is replaced with the corresponding sequence (e.g., ATGCTA). (B) Splitting: A contig is split into two sequences at the zero-coverage position. (C) Representative sequence selection: representative sequences are selected from a modified assembly (contigs in black color) combined with all/15X CPBLRs (in blue color). (D) Strict bridging (SB): a representative sequence (RS) is used for bridging if it uniquely (i.e. the length of end-to-end alignments (as bounded by the vertical bars) is maximal and at least 1.25-fold larger than the secondary choice) aligns to two representative sequences (either one must be a black representative contig). The grey lines represent connected sequences. (E) Easy bridging (EB): a representative CPBLR (in blue) is used for bridging if it aligns to two individual contig sequences (in black) at either end.