Comparison of k-mer-based de novo comparative metagenomic tools and approaches.

ABSTRACT: Aim: Comparative metagenomic analysis requires measuring a pairwise similarity between metagenomes in the dataset. Reference-based methods that compute a beta-diversity distance between two metagenomes are highly dependent on the quality and completeness of the reference database, and their application on less studied microbiota can be challenging. On the other hand, de-novo comparative metagenomic methods only rely on the sequence composition of metagenomes to compare datasets. While each one of these approaches has its strengths and limitations, their comparison is currently limited. Methods: We developed sets of simulated short-reads metagenomes to (1) compare k-mer-based and taxonomy-based distances and evaluate the impact of technical and biological variables on t

SUBMITTER: Ponsero AJ 

PROVIDER: S-EPMC10696585 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature