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Updated: May 12, 2026

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
Published on: August 20, 2021
Metagenomic Assembly and Gene Prediction
Bo Li1, Xue Yang2, Tongyi Zhao2
1Guangdong Basic Research Center of Excellence for Ecological Security and Green Development, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, China. libo01@gdut.edu.cn.
Abstract:
Metagenomic assembly and gene prediction connect quality-controlled reads to downstream microbiome analyses. This chapter outlines core assembly strategies, including per-sample versus co-assembly and short-read versus hybrid approaches, and highlights key parameters and metrics for evaluating assembly quality. Gene prediction from contigs and the construction of nonredundant gene catalogs are introduced as fundamental steps for representing community coding potential. The resulting contigs and gene sets provide essential input for metagenome-assembled genome (MAG) reconstruction, as well as taxonomic and functional annotation in subsequent chapters.
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