Inline Index Helped in Cleaning up Data Contamination Generated During Library Preparation and the Subsequent Steps
Abstract High-throughput sequencing involves library preparation and amplification steps, which may induce contamination across samples or between samples and the environment. We tested the effect of applying an inline-index strategy, in which DNA indices of 6 bp were added to both ends of the inserts at the ligation step of library prep for resolving the data contamination problem. Our results showed that the contamination ranged from 0.29–1.25% in one experiment and from 0.83–27.01% in the other. We also found that contamination could be environmental or from reagents besides cross-contamination between samples. Inline-index method is a useful experimental design to clean up the data and address the contamination problem which has been plaguing high-throughput sequencing data in many applications.