However, one serious drawback to larger multiplexing of indexed samples is index switching leading to the attribution of variants to the incorrect individual.
Sinha, R. et al. Index switching causes "spreading-of-signal" among multiplexed samples in Illumina HiSeq.
Sinha, R. Index switching causes "Spreading-Of-Signal" among multiplexed samples in Illumina HiSeq 4000 DNA sequencing.
Therefore, either some PCR primers containing a specific index were likely to have been contaminated into the tube, the index sequences had errors, and/or index switching might have happened in the sequencing step24.
We also showed quantitatively further functional advantages of the molecular barcodes: our molecular barcode was utilized in identification of sample cross-contamination (caused by physical contamination of primers, errors in indices, and/or index switching in the sequencing process) and misidentification of the target sequence in the alignment process.
The microstructural differences as a function of OAD content are reflected in the transmission modulation in the photopic and solar regions, NIR reflectance, optical absorption coefficient, band gap, refractive index, switching kinetics, charge storage capacity and electrochemical activity of the films.
We propose a mechanism for index switching in Additional file 1: Figure S13.
Our results suggest that index switching is a random and stochastic process resulting in approximately 3.4% of reads in the entire pool attributed to an incorrect index.
However, one serious potential drawback in integrating large scale indexing would be data contamination due to index switching, or the transfer of an index from one individual to the sequencing read of another individual.
