Figure 1.

Illustration of different constructs and the reads produced. Single-end data on top, paired-end below. Inserts are denoted I, single-end reads R and paired-end reads R1 and R2. Read length denoted L_R, insert length denoted L_I. A) L_I ≥ L_R: No adapter contamination. B) L_I < L_R: adapter contamination occurs in 3’ end. C) L_I ≥ 2· L_R: No adapter contamination and no overlap between reads. D) L_R < L_I < 2  · L_R: No adapter contamination but the two reads overlap. E) L_I < L_R: adapter contamination in 3’ ends of both reads, overlap between 5’ ends of reads. This information can be used to perform the pairwise alignment needed (after reverse complementing mate 2 from the pair) to locate adapter contamination and/or overlap between reads