Figure 4

Moving windows categorize each base call as bad (0) or good (1). Illustrated here is the function of moving_window (19,10,13/19), the last of four such moving windows. (A) Each base call and its associated quality score is determined with phred. A moving window categorizes each pivot base as either bad or good, resulting in a new quality category string consisting of 0 s or 1 s. Gap-Join/Seq-Merge evaluates gaps identified by two of the moving windows as described in the text. This algorithm then either joins two gaps to form a longer one (B) or, when the next fragment of good quality is at least twice as long as the preceding gap length, merges that gap into an extended good region (C).