rmvPFBAM: Removing Primers from BAM Files Based on Amplicon-Based Next-Generation Sequencing and Cloud Computing When Analyzing Personal Genome Data

Table 1

Comparative data among the three tools by using six samples from amplicon-based next-generation sequencing data.

Sample (no. of paired reads)	Parameter	CutPrimers (err = 3, threads = 4)	BAMClipper (with –g)	rmvPFBAM (err = 3)
SRR866441 (2238436); SRR866442 (2738246); SRR866443 (2628572); SRR866444 (3586450); SRR866445 (2760844); SRR948507 (2749834)	Time of running(s)	451; 507; 485; 672; 513; 525	869; 1135; 1052; 1467; 1148; 1149	121; 159; 150; 229; 149; 164
SRR866441 (2238436); SRR866442 (2738246); SRR866443 (2628572); SRR866444 (3586450); SRR866445 (2760844); SRR948507 (2749834)	No. of paired reads after cutting primers (%)	_	2238436(100); 2738246(100); 2628572(100); 3586450(100); 2760844(100); 2749834(100)	1840262(82.2); 2518726(92.0); 2320172(88.3); 3342890(93.2); 2380948(86.2); 2430968(88.4)
SRR866441 (2238436); SRR866442 (2738246); SRR866443 (2628572); SRR866444 (3586450); SRR866445 (2760844); SRR948507 (2749834)	No. of target region reads after cutting primers (%)	_	1882305(84.1); 2609012(95.3); 2365634(90.0); 3390685(94.5); 2424973(87.8); 2473225(89.9)	1840262(82.2); 2518726(92.0); 2320172(88.3); 3342890(93.2); 2380948(86.2); 2430968(88.4)
SRR866441 (2238436); SRR866442 (2738246); SRR866443 (2628572); SRR866444 (3586450); SRR866445 (2760844); SRR948507 (2749834)	No. of nontarget region reads after cutting primers (%)	_	269848(12.1); 103128(3.8); 186292(7.1); 161479(4.5); 254749(9.2); 221905(8.1)	0; 0; 0; 0; 0; 0
SRR866441 (2238436); SRR866442 (2738246); SRR866443 (2628572); SRR866444 (3586450); SRR866445 (2760844); SRR948507 (2749834)	No. of mutations detected based on the cutting primer BAM	_	981; 527; 584; 544; 847; 793	676; 329; 398; 349; 515; 488
SRR866441 (2238436); SRR866442 (2738246); SRR866443 (2628572); SRR866444 (3586450); SRR866445 (2760844); SRR948507 (2749834)	No. of mutations based on the cutting primer BAM (fall in target region)	_	727; 351; 415; 361; 552; 527	676; 329; 398; 349; 515; 488