Figure 1From: AdapterRemoval: easy cleaning of next-generation sequencing readsIllustration 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 R 1 and R 2. 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 readsBack to article page