Why the whole read has to be clipped when the technical sequence overlap or partial overlap with the 5' end of the read?
Figure 1 illustrates the alignments tested for each technical sequence. The process begins with a partial overlap of the 3′ end of the technical sequence with the 5′ end of the read, as shown in (A). Testing proceeds by moving the putative contaminant toward the 3′ end of the read. In both the partial overlap (A) and complete overlap at the 5′ end (B) scenarios, the entire read will be clipped. If the contaminant is found within the read (C), the bases from the 5′ end of the read to the beginning of the alignment are retained. The testing process continues until only a partial alignment on the 3′ end of the read remains (D).