Table 2.

Effects of mismatches on the performance of Alientrimmer, Cutadapt, cutPrimers and pTrimmer. with a simulation datasets (100×). Sensitivity (True Positive Rate, TPR) represent the proportion of reads whose primers were removed, in part or in full, by the programs in the reads that have primers introduced during simulation. Specificity (True Negative Rate, TNR) represent the proportion of reads for whom no primers were identified by the program in the reads that have no primers introduced during simulation. Accuracy (ACC) represent the proportion of reads whose primer sequences were precisely trimmed. Testing was performed with a simulation dataset of 100× depth with 1 ~ 5 mismatches allowed

Mismatch	Alientrimmer 1 threads, K = 9	Cutadapt 8 threads	cutPrimers 8 threads	pTrimer 2 threads, k = 9
	TPR (%)/TNR (%)/ACC (%)	TPR (%)/TNR (%)/ACC (%)	TPR (%)/TNR (%)/ACC (%)	TPR (%)/TNR (%)/ACC (%)
1	100.00/0.00/2.48	100.00/98.42/0.00	56.56/100.00/56.56	99.22/100.00/98.87
2	100.00/0.00/0.91	100.00/98.42/0.00	64.08/100.00/57.77	99.96/100.00/99.38
3	100.00/0.00/0.40	100.00/45.79/0.00	67.44/100.00/58.32	99.94/100.00/99.13
4	100.00/0.00/0.00	100.00/44.74/0.00	70.85/100.00/58.73	99.67/100.00/98.60
5	100.00/0.00/0.00	100.00/23.16/0.00	70.77/100.00/57.46	98.88/100.00/97.63