Fig. 5
From: Quality filtering of Illumina index reads mitigates sample cross-talk
Recommended procedure for removing background reads. a When using unique dual index sequences for every sample (si), each missing index pair offers a negative control that provides an estimate of the number of misassigned reads (ε). b When almost all index combinations are being used, controls can be added by purposefully omitting samples for some combinations of index sequences. c The quality score threshold (Qthresh) can then be optimized by plotting the sum of misassignments versus the number of reads remaining. d A value of Qthresh can be selected that minimizes misassignments while maximizing the number of reads that remain