Using strain-resolved analysis to identify contamination in metagenomics data.

ABSTRACT:

Background

Metagenomics analyses can be negatively impacted by DNA contamination. While external sources of contamination such as DNA extraction kits have been widely reported and investigated, contamination originating within the study itself remains underreported.

Results

Here, we applied high-resolution strain-resolved analyses to identify contamination in two large-scale clinical metagenomics datasets. By mapping strain sharing to DNA extraction plates, we identified well-to-well contamination in both negative controls and biological samples in one dataset. Such contamination is more likely to occur among samples that are on the same or adjacent columns or rows of the extraction plate than samples that are far apart. Our strain-resolved workflow also reveals the presence

SUBMITTER: Lou YC 

PROVIDER: S-EPMC9979413 | biostudies-literature | 2023 Mar

REPOSITORIES: biostudies-literature