Metagenomic Data Analysis

This volume describes different sequencing methods, pipelines and tools for metagenome data analyses. Chapters guide readers through quality control of raw sequence data, metagenomics databases for bacterial annotations suchGreengenes, SILVA, RDP and GTDB, guide to 16S rRNA microbiome analysis and pipelines such asmothur, DADA2,QIIME2, whole genome shotgun metagenomics data analyses pipeline using MEGAN and DIAMOND, web service such as PATRIC, RDP, mothur, Kaiju, PhyloPythiaS, MG-RAST, WebMGA, MicrobiomeAnalyst, WHAM!, METAGENassist and MGnify: EBI-Metagenomics, MG-RAST Metagenomics Analysis. Then the chapters inform the readers regarding Third-generation sequencing (TGS) approachesas MinION sequencing and teaches use ofUbuntu Linux Virtual Machine configuration, clinical and environmental resistomes, use of FISH techniques and designing FISH probes, protocols for viral metagenomics, and comprehensive guideline for microbiome analysis usingmost used R packages. Written in the format of the highly successfulMethods in Molecular Biologyseries, each chapter includes an introduction to the topic, lists necessary materials and methods, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge,Metagenomic Data Analysis: Methods and Protocols aims to be comprehensive guide for researchers to specialize in the metagenomics field.