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Table 2 Number of simulated differences (Truth) and differences obtained by NucDiff, dnadiff and QUAST

From: NucDiff: in-depth characterization and annotation of differences between two sets of DNA sequences

Group Truth NucDiff dnadiff QUAST
nonTandem 3448 6717 7460 2814
Tandem 119 116 116 0
Substitutions 164 423 234 354
Relocations 2854 2802 2211 185
Translocations 163 137 137 117
Inversions 1068 1060 1060 1053
UnalignedSeq 13 21 16 21
  1. In the nonTandem group, the values shown for the simulated differences (Truth) and QUAST are the number of events, while in the other columns the values are the sum of the number of bases involved in the differences for short and medium local differences (found by the show-snps program) and the number of events of long local differences (those causing alignment fragmentation). In the Inversions group, the numbers of simulated inversions and inversions found by NucDiff were multiplied by two to enable a fair comparison, because QUAST and dnadiff report the number of fragment ends, while NucDiff reports the number of fragments. In the Substitutions group, the values shown are the number of bases, while in the other rows the values are the number of events. The reshuffling differences are contained in the nonTandem group for QUAST, but placed in the Relocations group in all other cases