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) |