EukRep

EukRep classifies eukaryotic sequences in metagenomic datasets using a k-mer-based strategy to separate eukaryotic from prokaryotic fragments and enable genome recovery and metabolic analysis.

Key Features:

• K-mer-based classification: Implements a k-mer–based strategy to classify sequence fragments as eukaryotic or prokaryotic.
• Eukaryotic sequence identification: Distinguishes eukaryotic and prokaryotic fragments within mixed metagenomic data to facilitate extraction of eukaryotic sequences.
• Genome recovery and completeness evaluation: Supports reconstruction of near-complete eukaryotic genomes, demonstrated by recovery of three fungi (Eurotiomycetes) and an arthropod.
• Metabolic potential prediction: Enables downstream prediction of metabolic functions and detection of community metabolic shifts, as observed after organic carbon addition with increased secreted proteases, lipases, cellulose-targeting CAZymes, and methanol oxidation.
• Application to environmental samples: Applied to complex environmental datasets to reconstruct and evaluate high-quality genomes from fungi, protists, and rotifers for cultivation-independent community analyses.

Scientific Applications:

• Ecosystem and microbial community studies: Integrates eukaryotic sequences into metagenomic analyses to improve interpretation of microbial community dynamics and functions.
• Genome-resolved environmental genomics: Enables cultivation-independent reconstruction of near-complete eukaryotic genomes from environmental samples such as geyser-associated microbial communities.
• Metabolic response analysis: Detects metabolic shifts in eukaryotic populations under environmental perturbations, exemplified by changes after organic carbon addition (secreted proteases, lipases, CAZymes, methanol oxidation).
• Taxonomic recovery across eukaryotes: Facilitates recovery and evaluation of genomes from diverse eukaryotes including fungi, protists, rotifers, and arthropods.

Methodology:

Classifies sequence fragments using a k-mer-based strategy to separate eukaryotic from prokaryotic sequences.