Inline index helped in cleaning up data contamination generated during library preparation and the subsequent steps

Abstract

Background: High-throughput sequencing involves library preparation and amplification steps, which may induce contamination across samples or between samples and the environment.

Methods: 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.

Results: Our results showed that the contamination ranged from 0.29 to 1.25% in one experiment and from 0.83 to 27.01% in the other. We also found that contamination could be environmental or from reagents besides cross-contamination between samples.

Conclusions: 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.

Keywords: Contamination; Cross-contamination; Environmental DNA; Indexing; Meta genomics; Multiplexed sequencing; Next-generation sequencing; Phylogenomics.