数字农科院2.0

Computational Tools and Resources for Long-read Metagenomic Sequencing Using Nanopore and PacBio

文献类型： 外文期刊

作者： Tianyuan Zhang;Mian Jiang;Hanzhou Li;Yunyun Gao;Salsabeel Yousuf;Kaimin Yu;Xinxin Yi;Jun Wang;Lulu Yang;Yong Xin Liu

作者机构：

关键词： Database;Metagenome;Nanopore;PacBio;Software

期刊名称： Genomics, Proteomics and Bioinformatics

ISSN： 1672-0229

年卷期： 2025 年 23 卷 4 期

页码：

收录情况： SCIE（2025版） ; ; CSCD（2025-2026年度） ; ; 科技核心（2024版）

摘要： In recent years, the field of shotgun metagenomics has witnessed remarkable advancements, primarily driven by the development and refinement of next-generation sequencing technologies, particularly long-read sequencing platforms such as Nanopore and PacBio. These platforms have significantly improved the ability to analyze microbial communities directly from environmental samples, providing valuable information on their composition, function, and dynamics without the need for pure cultivation. These technologies enhance metagenomic data assembly, annotation, and analysis by addressing longer reads, higher error rates, and complex data. In this review, we provide a comprehensive overview of the historical development of long-read metagenomics, highlighting significant landmarks and advancements. We also explore the diverse applications of long-read metagenomics, emphasizing its impact across various fields. Additionally, we summarize the essential computational tools and resources, including software, databases, and packages, developed to enhance the efficiency and accuracy of metagenomic analysis. Finally, we provide a practical guide for the installation and use of notable software available on GitHub (https://github.com/zhangtianyuan666/ LongMetagenome). Overall, this review assists the metagenomics community in exploring microbial life in unprecedented depth by providing a roadmap for successful resource utilization and emphasizing possibilities for innovation.

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