Editing assembly graphs. Assembly graphs are edited to improve their quality. (A) Clean-up operations, for example, removal of short “hanging ends,” like the middle vertical edge; other clean-up operations include deletion of sequence that is not covered by paired reads and deletion of tiny graph components. (B) Disambiguation operations. Here, given sufficient paired-read links from the left to the right edge, the precise number of copies of the loop edge may be determined, and it may then be unrolled, thereby replacing all three edges by a single edge. (C) Pulling-apart operations. If paired-read links go from the left red edge to the right red edge, and from the left black edge to the right black edge, but not from red to black or black to red, the middle edge may be duplicated, yielding as output two composite edges.
