Affiliation:
1. Korean Medicine Data Division, Korea Institute of Oriental Medicine , Daejeon , Republic of Korea
2. Department of Systems Biotechnology, Chung-Ang University , Anseong , Republic of Korea
Abstract
Abstract
Microbial genome recovery from metagenomes can further explain microbial ecosystem structures, functions and dynamics. Thus, this study developed the Additional Clustering Refiner (ACR) to enhance high-purity prokaryotic and eukaryotic metagenome-assembled genome (MAGs) recovery. ACR refines low-quality MAGs by subjecting them to iterative k-means clustering predicated on contig abundance and increasing bin purity through validated universal marker genes. Synthetic and real-world metagenomic datasets, including short- and long-read sequences, evaluated ACR's effectiveness. The results demonstrated improved MAG purity and a significant increase in high- and medium-quality MAG recovery rates. In addition, ACR seamlessly integrates with various binning algorithms, augmenting their strengths without modifying core features. Furthermore, its multiple sequencing technology compatibilities expand its applicability. By efficiently recovering high-quality prokaryotic and eukaryotic genomes, ACR is a promising tool for deepening our understanding of microbial communities through genome-centric metagenomics.
Funder
Korea Environment Industry & Technology Institute
Core Technology Development Project for Environmental Disease Prevention and Management
Korea Ministry of Environment
Korea Health Industry Development Institute
Ministry of Health and Welfare
Publisher
Oxford University Press (OUP)
Subject
Molecular Biology,Information Systems