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Updated: Sep 26, 2025

Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples
Published on: December 22, 2014
Recovering metagenome-assembled genomes from shotgun metagenomic sequencing data: Methods, applications, challenges,
Yunyan Zhou1, Min Liu2, Jiawen Yang2
1State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang 330045, China; Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China.
Abstract:
Reference genomes are essential for analyzing the metabolic and functional potentials of microbiomes. However, microbial genome resources are limited because most of microorganisms are difficult to culture. Genome binning is a culture-independent approach that can recover a vast number of microbial genomes from short-read high throughput shotgun metagenomic sequencing data. In this review, we summarize methods commonly used for reconstructing metagenome-assembled genomes (MAGs) to provide a reference for researchers to choose propriate software programs among the numerous and complicated tools and pipelines that are available for these analyses. In addition, we discuss application prospects, challenges, and opportunities for recovering MAGs from metagenomic sequencing data.
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