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Table 1 Benchmarks of four programs with three multiplex amplicon sequencing datasets. ‘Trimmed Reads’ indicates the reads that had any number of bases removed by the program. ‘Precisely Trimmed Reads’ indicates the reads whose primer sequences were precisely trimmed. K: the number of nucleotides for “k-mer” algorithm. Err: the number or percentage of allowed mismatches for primer searching. See Additional file 1 for the detailed parameters to run each of these programs

From: pTrimmer: An efficient tool to trim primers of multiplex deep sequencing data

Sample (No. of reads)   Alientrimmer Cutadapt cutPrimers  
Parameter 1 thread, K = 9, err = 3 8 threads, err = 10% 8 threads, err = 3 2 threads, k = 9, err = 3
CfDNA1 (11,498,560) Time of 1137 108,918 2224 35
CfDNA2 (16,694,386) Running (s) 2511 170,920 3646 47
CfDNA3 (36,119,764)   6099 349,789 7772 62
CfDNA1 (11,498,560) No. of 2,228,698 (19.28) 11,392,006 (99.07) 8,733,142 (75.95) 10,973,548 (95.43)
CfDNA2 (16,694,386) Trimmed Reads (%) 3,193,584 (19.13) 16,633,850 (99.64) 12,481,890 (74.77) 16,023,158 (95.98)
CfDNA3 (36,119,764)   5,680,392 (15.73) 35,921,534 (99.45) 24,460,516 (67.72) 32,314,848 (89.47)
CfDNA1 (11,498,560) No. of 81,143 (0.71) 389,526 (3.39) 7,752,109 (67.42) 10,908,534 (94.87)
CfDNA2 (16,694,386) Precisely Trimmed Reads (%) 134,647 (0.81) 516,377 (3.09) 11,130,147 (66.67) 5,905,037 (95.27)
CfDNA3 (36,119,764)   236,252 (0.65) 1,003,057 (2.78) 21,581,726 (59.75) 12,024,840 (88.66)