Figure 3. Comparative view of a transposase-rich region of the M. tuberculosis F11 genome (coordinates 1,991,000 to 2,006,300) obtained from the draft (A) and Pilon-improved (B) assemblies.

In the draft assembly, three regions containing transposases (shown in blue) remained unassembled resulting in gaps. In the Pilon-improved assembly, all three sets of transposases were successfully assembled. The Pilon-improved assembly also contained a hypothetical gene, TBFG_11790 (shown in red), missing from the draft assembly. Though TBFG_11790 was not fully closed in the Pilon-improved version, closer inspection revealed that there was a 42 bp overlap in assembled sequence at this site. By default, Pilon will not close gaps unless there is at least 95 bp overlapping sequence to minimize spurious joins.