Techniques for analyzing and quantifying sample bleed through in genotyping with Illumina
Are you using dual-index barcodes with different barcodes at each end? There is a known phenomena of "index switching" that occurs in Illumina reads. One way to control for this is to add in unamplified water samples that have unused barcode combinations where each of the indexes is shared with another sample.

More information can be found on this SeqAnswers thread. Here are some useful associated links:


Signal-spreading preprint -- detailed investigation of the phenomenom, including methods, graphs, and associated data
Crossblock -- tool by Brian Bushnell that attempts to remove cross contamination
Summary by James Hadfield -- mentions a few fixes suggested by Illumina, many centred around not using barcode combinations that could conflict
Illumina's quick-fire response -- they've known about it for a long time, and point out that it shouldn't be a problem for most purposes


I have suspicions that at least some of the index switching is being caused by ligation of two separate barcoded fragments during the sample prep (which definitely happens during sample prep for nanopore), but I haven't done any experimentation to work out if this is also the case for Illumina (due to money/time/goal constraints). The experimental design would be to take a prepared Illumina library just prior to sequencing, ligate on ONT adapters, then sequence on both the ONT and Illumina machines to see if chimeric reads discovered via nanopore sufficiently matches the index switching observed via short-read sequencing.