The rolling-phrap process limits the scope of reads presented to Phrap in each wave. All reads for an eBAC are added in the first wave including that eBAC. Contigs are recorded in an .ace file, and the corresponding reads are removed from the Phrap input, until a contig contains (almost) no reads from eBACs overlapping the next wave. (1) First wave containing all eBACs overlapping leftmost eBAC (arrow); (2) emit pure leftmost-eBAC contigs (not overlapping and therefore not merged with any other eBAC); (3) second wave containing all eBACs overlapping next leftmost eBAC contributing new sequences; (4) emit contigs solely from first-wave eBAC regions; (5) third wave containing all eBACs overlapping next leftmost eBAC contributing new sequences; (6) emit new contigs solely from first and second-wave eBAC regions; (7) fourth wave; (8) emit remaining contigs.
