Figure 2From: AdapterRemoval: easy cleaning of next-generation sequencing readsThe need for shifting the alignment due to missing nucleotides. If the read is missing a few nucleotides in the 5’ end, the proper alignment will not be recoverable if the procedure stops at the first position. As shown in 1), this leads to multiple mismatches and possibly missed adapter contamination. If the alignment is shifted by S nucleotides as shown in 2), the correct alignment can be found. The dynamic programming matrix in 3) shows which entries in the matrix leads to the two solutions shown here. The light grey part is the upper half of the matrix that is calculated by default; the two dark grey entries illustrate the two alignments shown in 1) and 2)Back to article page