Fig. 1

Illustrations of the approaches discussed in the “Background” section. The similar repeat based alignment approach, the long read support based validation approach and the adjacent alignment based validation approach are illustrated in (1), (2) and (3), respectively. (1) Long read region A in r ₁ does not have its true genome region in contig c ₁, but it could be aligned to its similar repeat B (shaded), which is the true genome region of long read region B in contig c ₁. (2) Adjacent long read regions A and B in r ₁ are aligned to contig region A in c ₁ and contig region B in c ₂, respectively. These alignments are accepted after validation with a sufficient number of long reads r ₁, r ₂, r ₃ and r ₄ supporting them. (3) Adjacent long read regions A and B in r ₁ are aligned to the adjacent contig regions A and B in c ₁, respectively, and are thus accepted after validation