Fig. 1

The schematic framework of GAAP. seg, segment of cGOF. ref, reference; sc, scaffold/contig (assemblies). Head (filled circle) and tail (empty circle) vertices of the syntenic seg in each reference are sequentially connected with a dashed line indicating the seg permutation (order and orientation). The sc are indexed with seg and merged into ordered sc “strings”. The graph in the local scaffolding of ordered sc is built by connecting seg-ordered sc and unordered sc, where the PE links are higher than a certain cut-off. The line widths indicate the link count. Pseudo-genome of draft-quality assembly is constructed by combining the indexed scaffolds and the closest relevant seg permutaion of references