A critical assessment of gene catalogs for metagenomic analysis.

ABSTRACT:

Motivation

Microbial gene catalogs are data structures that organize genes found in microbial communities, providing a reference for standardized analysis of the microbes across samples and studies. Although gene catalogs are commonly used, they have not been critically evaluated for their effectiveness as a basis for metagenomic analyses.

Results

As a case study, we investigate one such catalog, the Integrated Gene Catalog (IGC), however, our observations apply broadly to most gene catalogs constructed to date. We focus on both the approach used to construct this catalog and on its effectiveness when used as a reference for microbiome studies. Our results highlight important limitations of the approach used to construct the IGC and call into question the broad usefulness of

SUBMITTER: Commichaux S 

PROVIDER: S-EPMC8479683 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature