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Table 1 Sensitivity and precision of each pipeline (mean [95% CI])

From: Detection of low-density Plasmodium falciparum infections using amplicon deep sequencing

 

DADA2

HaplotypR

PASEC

SeekDeep1x

SeekDeep2x

All samples

 Sensitivity

  All

0.66 [0.62, 0.70]

0.66 [0.62, 0.70]

0.71 [0.68, 0.75]

0.72 [0.68, 0.76]

0.62 [0.56, 0.68]

  CSP

0.66 [0.61, 0.71]

0.64 [0.59, 0.70]

0.70 [0.64, 0.75]

0.70 [0.65, 0.75]

0.61 [0.53, 0.69]

  SERA2

0.65 [0.59, 0.70]

0.68 [0.62, 0.74]

0.73 [0.68, 0.78]

0.73 [0.68, 0.79]

0.63 [0.55, 0.71]

 Precision

  All

0.81 [0.77, 0.84]

0.88 [0.85, 0.90]

0.81 [0.78, 0.85]

0.25 [0.23, 0.27]

0.68 [0.63, 0.74]

  CSP

0.72 [0.67, 0.77]

0.94 [0.91, 0.97]

0.86 [0.81, 0.89]

0.26 [0.23, 0.28]

0.77 [0.69, 0.84]

  SERA2

0.91 [0.87, 0.94]

0.82 [0.78, 0.86]

0.77 [0.72, 0.82]

0.25 [0.22, 0.28]

0.61 [0.53, 0.68]

Samples with ≥ 100 reads

 Sensitivity

  All

0.83 [0.80, 0.86]

0.84 [0.81, 0.86]

0.83 [0.81, 0.86]

0.83 [0.80, 0.86]

0.78 [0.78, 0.87]

  CSP

0.82 [0.78, 0.86]

0.82 [0.77, 0.86]

0.82 [0.78, 0.86]

0.82 [0.78, 0.86]

0.84 [0.78, 0.89]

  SERA2

0.85 [0.80, 0.89]

0.86 [0.81, 0.90]

0.85 [0.80, 0.89]

0.85 [0.81, 0.89]

0.82 [0.75, 0.88]

Precision

  All

0.83 [0.80, 0.86]

0.89 [0.87, 0.92]

0.92 [0.90, 0.94]

0.26 [0.24, 0.28]

0.79 [0.74, 0.84]

  CSP

0.75 [0.70, 0.79]

0.94 [0.91, 0.96]

0.95 [0.92, 0.97]

0.27 [0.24, 0.30]

0.88 [0.83, 0.93]

  SERA2

0.92 [0.88, 0.95]

0.84 [0.80, 0.88]

0.90 [0.86, 0.93]

0.25 [0.22, 0.28]

0.71 [0.63, 0.78]