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).