Improved eukaryotic detection compatible with large-scale automated analysis of metagenomes.

ABSTRACT:

Background

Eukaryotes such as fungi and protists frequently accompany bacteria and archaea in microbial communities. Unfortunately, their presence is difficult to study with "shotgun" metagenomic sequencing since prokaryotic signals dominate in most environments. Recent methods for eukaryotic detection use eukaryote-specific marker genes, but they do not incorporate strategies to handle the presence of eukaryotes that are not represented in the reference marker gene set, and they are not compatible with web-based tools for downstream analysis.

Results

Here, we present CORRAL (for Clustering Of Related Reference ALignments), a tool for the identification of eukaryotes in shotgun metagenomic data based on alignments to eukaryote-specific marker genes and Markov clustering. Usi

SUBMITTER: Bazant W 

PROVIDER: S-EPMC10084625 | biostudies-literature | 2023 Apr

REPOSITORIES: biostudies-literature