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. 2014 Nov 10;9(11):e112950. doi: 10.1371/journal.pone.0112950

Table 1. Comparison between different methods and technologies based on relative coverage (RC) analysis of the data.

Ion Torrent PGM
RC Standard no library amplification Covaris NEBNext ds Fragmentase
Total Plus Min Total Plus Min Total Plus Min Total Plus Min
<0.5 15.14 23.43 3.96 16.10 24.32 4.64 13.15 22.33 2.58 11.17 19.25 1.60
<0.25 1.36 13.12 0.02 1.10 13.73 0.09 0.88 12.70 0.35 0.27 11.52 0.29
<0.10 0.01 7.66 0.01 0.04 8.38 0.04 0.01 7.83 0.01 0.00 7.05 0.01
<0.05 0.00 5.47 0.01 0.00 6.02 0.01 0.00 5.81 0.01 0.00 4.95 0.00
<0.01 0.00 2.04 0.00 0.00 2.49 0.00 0.00 2.73 0.00 0.00 1.96 0.00
Illumina MiSeq
RC TruSeq-Covaris TruSeq-NEBNext ds Fragmentase Nextera XT
Total Plus Min Total Plus Min Total Plus Min
<0.5 0.27 1.56 1.47 0.39 1.64 1.14 7.03 9.20 9.57
<0.25 0.01 0.81 0.83 0.01 0.73 0.42 1.64 2.61 2.48
<0.10 0.01 0.38 0.35 0.01 0.12 0.02 0.01 0.26 0.01
<0.05 0.00 0.23 0.20 0.00 0.01 0.00 0.01 0.06 0.01
<0.01 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00

For all samples processed with a same protocol the average relative coverage was calculated and resulted in 7 different datasets. For each dataset, the fraction with a relative coverage <0.50, <0.25, <0.10, <0.05, <0.01 was determined. These analyses were performed for each strand separately (Plus, Min) and the total relative coverage (Total).