De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae

For Pto_DC3000, the effect of error correction on total numbers of errors in Newbler scaffolds. Cases where repeat regions (see Fig. 2; Supplemental Fig. 2) were detected are noted. In the case of SNPs, conflicting votes lead to replacement with an ambiguous base pair. In the case of repeat regions (i.e., rearrangements), regions are noted but are not removed from the genome. In Pto_DC3000, the number of SNPs and rearrangements fixed with this method and the effect of these corrections on gene prediction are also shown. For Por_{1_6}, only the number of corrections made can be measured.