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Table 2 Performance comparison of Bustard, Ibis and AYB on several sets of reads of varying read length and chemistry versions.

From: All Your Base: a fast and accurate probabilistic approach to base calling

   Reads mapped, %    Reads perfect, %  
  Bustard Ibis Δ% AYB Δ% Bustard Ibis Δ% AYB Δ%
ϕX174 L2 76.62 78.33 +2.23 78.25 +2.13 55.88 58.94 +5.48 62.29 +11.48
ϕX174 L4 63.02 66.11 +4.90 65.09 +3.29 40.09 43.08 +7.46 44.74 +11.60
ϕX174 L6 72.09 74.07 +2.75 74.08 +2.77 51.19 53.34 +4.20 56.00 +9.40
Ibis Test 84.77 88.45 +4.34 88.19 +4.03 44.34 66.14 +49.16 69.32 +56.34
B. pert./1 28.76 39.16 +35.94 45.80 +58.98 2.53 3.14 +23.70 4.13 +62.86
... trimmed 77.35 81.06 +4.80 81.14 +4.90 39.52 47.64 +20.55 55.24 +39.79
B. pert./2 34.33 47.41 +38.75 53.50 +55.57 6.22 17.69 +183.98 26.67 +327.97
... trimmed 66.54 70.22 +5.53 72.07 +8.31 30.13 40.72 +35.18 48.25 +60.15
BGI/1 87.41 89.01 +1.82 88.85 +1.64 59.62 68.39 +14.70 69.29 +16.22
BGI/2 84.58 86.29 +2.03 86.52 +2.29 55.95 61.90 +10.64 63.30 +13.14
Illumina/1 97.58 97.80 +0.22 97.85 +0.28 72.55 75.80 +4.49 76.70 +5.73
Illumina/2 96.29 96.73 +0.46 96.82 +0.55 70.61 73.88 +4.63 74.66 +5.74
HiSeq/1 84.97 85.24 +0.32 85.97 +1.18 60.29 62.55 +3.75 64.50 +6.98
HiSeq/2 79.78   81.34 +1.76 49.79   55.58 +11.63
  1. Performance is compared in terms of the percentage of reads mapped back to the reference with five edits or fewer, and the percentage of reads which perfectly match the reference; the 'Δ%' figures for Ibis and AYB, where given, are the percentage improvements over Bustard. See text for further details. †Ibis failed to process the second end of the HiSeq data.