Merging into a raft. A contig (‘raft’) of three sequences: A, B, and C has already been constructed by GigAssembler. The program now examines an alignment between sequence C and a new sequence, D, to see whether D should also be added to the raft. The parts of D marked with +s are compatible with the raft because of the C/D alignment. The program must also check that the parts of D marked with ?s are compatable with the raft by examining other alignments.