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This chapter presents current best practices for the bioinformatic analysis of Whole Metagenome Sequencing (WMS) datasets discussing key methodological challenges. Read-based analysis of WGS enables the taxonomic classification and functional profiling through comparison of the sequencing reads against reference databases with assembly-based analysis allowing recovery of metagenome-assembled genomes (MAGs). Together, both approaches offer a complementary insight into the microbiome and require users to navigate the vast number of tools and methodologies published. Practical recommendations for tool selection and parameter optimization, considering computational requirements and biological accuracy, are included throughout.

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Bioinformatics Processing of Whole Metagenome Shotgun Datasets

  • 实验方案

  • 出版模式：

    开放获取

  • 发表日期：

    2026年

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  • Anthony Duncan,
  • Wing Koon,
  • Katarzyna Sidorczuk,
  • Alise J. Ponsero,
  • Sumeet K. Tiwari,
  • Falk Hildebrand,
  • Andrea Telatin

摘要

This chapter presents current best practices for the bioinformatic analysis of Whole Metagenome Sequencing (WMS) datasets discussing key methodological challenges. Read-based analysis of WGS enables the taxonomic classification and functional profiling through comparison of the sequencing reads against reference databases with assembly-based analysis allowing recovery of metagenome-assembled genomes (MAGs). Together, both approaches offer a complementary insight into the microbiome and require users to navigate the vast number of tools and methodologies published. Practical recommendations for tool selection and parameter optimization, considering computational requirements and biological accuracy, are included throughout.