PVAmpliconFinder: a workflow for the identification of human papillomaviruses from high-throughput amplicon sequencing

Table 1 Summary of the number of individual sequences considered at each step of the workflow

Step	Total sequencing raw reads	TrimGalore		Merging		Dereplication		Chimeric identification		Clustering		Papillomaviridae best hit (eval < =1e-5)		Defined group (same best hit)
Step	Total sequencing raw reads	TrimGalore		Merging		Dereplication		Chimeric identification		Clustering		Papillomaviridae best hit (eval < =1e-5)		Putative new (> 10% dissimilarity)		Putative known (< 10% dissimilarity)
Samples	N paired-end reads	N paired-end reads	%	N sequences	%	N sequences	%	N sequences	%	N sequences	%	N sequences	%	N sequences	%	N sequences	%
S1	564,435	564,064	99.93	551,266	97.73	22,551	4.09	22,498	99.76	79	0.35	61	77.22	0	0	5	8.20
S2	62,148	61,708	99.29	58,031	94.04	3281	5.65	3268	99.60	162	4.96	138	85.19	0	0	6	4.35
S3	316,297	315,999	99.91	307,400	97.28	15,562	5.06	15,562	100.00	51	0.33	49	96.08	1	2.04	18	36.73
S4	109,441	109,326	99.89	106,406	97.33	4842	4.55	4822	99.59	62	1.29	62	100.00	0	0	28	45.16
S5	309,779	309,390	99.87	294,563	95.21	14,101	4.79	14,091	99.93	140	0.99	129	92.14	2	1.55	39	30.23
S6	554,415	551,742	99.52	331,648	60.11	13,820	4.17	19,738	99.41	1162	8.46	910	78.31	0	0	16	1.76
S7	470,655	467,944	99.42	421,764	90.13	28,729	6.81	28,659	99.76	609	2.12	513	84.24	0	0	16	3.12
S8	263,707	263,270	99.83	244,177	92.75	13,293	5.44	13,283	99.92	194	1.46	188	96.91	0	0	8	4.26
Total number of sequences	2,650,877	2,643,443	99.72	2,315,255	87.58	116,179	5.02	115,921	99.78	2459	2.12	2050	83.37	3	0.45	136	16.73

ISSN: 1471-2105