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Table 3 Main features of Illumina MiSeq sequencing Run obtained after Trimmomatic, SPADES and SAMtools application

From: Detection of low-level HCV variants in DAA treated patients: comparison amongst three different NGS data analysis protocols

  Total reads Total reads after Trimmomatic Total reads after SPADES Number of reads aligned
1 (BL) 5,470,168 5,220,204 5,219,176 NS3 88,766
NS5A 2,952,378
NS5B 1,722,432
1 (FA) 839,254 622,494 619,064 NS3 30,329
NS5A 232,894
NS5B 273,387
2 (BL) 4,422,614 4,248,300 4,207,974 NS3 2,184,866
NS5A 1,476,874
NS5B 136,248
2 (FA) 3,956,108 3,726,938 3,677,042 NS3 455,654
NS5A 1584.345
NS5B 1,251,540
3 (BL) 3,956,876 3,611,990 3,535,350 NS3 244,237
NS5A 649,235
NS5B 1,746,295
3 (FA) 3,910,498 3,669,880 3,607,316 NS3 80,326
NS5A 166,688
NS5B 3,136,304
4 (BL) 3,830,412 3,636,298 3,591,446 NS3 30,775
NS5A 1,416,729
NS5B 1,925,610
4 (FA) 3,745,704 3,590,586 3,555,526 NS3 112,212
NS5A 1,284,284
NS5B 1,967,277
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