[i] ^aDistinct WGS in all overlaps produced by the overlapper with 95% identity and 100 k-mer copies allowed.

[ii] ^bFiltering done in Binner based only on overlapper information. Repeat heuristic limits k-mer copies to 12 (three times the coverage). Overlap quality heuristic requires 3 x span/(3+span-score)≥35, where score is the banded alignment score, and 2 x span/(2+span-score) would approximate the average distance between discrepancies were there only substitutions (indels have added penalties).

[iii] ^cBeyond the k-mer repeat and quality heuristics, only the top six (i.e., coverage × 1.5) WGS overlaps from each end of a BAC read are examined, and they are kept only if strictly better by the quality heuristic than the top discarded overlap.