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 such Greengenes, SILVA, RDP and GTDB, guide to 16S rRNA microbiome analysis and pipelines such as mothur, 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) approaches as MinION sequencing and teaches use of Ubuntu 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 successful Methods in Molecular Biology series, 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.

 

From genomics to metagenomics in the era of recent sequencing technologies.- Quality Control in Metagenomics Data.- Metagenomics Databases for Bacteria.- Amplicon Sequencing Pipelines in Metagenomics.- A practical guide to 16S rRNA microbiome analysis in musculoskeletal disorders.- DIAMOND+MEGAN microbiome analysis.- Interactive Web-based Services for Metagenomic Data Analysis and Comparisons.- Application of High Throughput Sequencing (HTS) to Enhance the Well-being of an Endangered Species (Malayan tapir): Characterization of Gut Microbiome using MG-RAST.- Designing knowledge-based bioremediation strategies using metagenomics.- Nanopore sequencing techniques – A comparison of the MinKNOW and the Alignator sequencers.- MAIRA: protein-based analysis of MinION reads on a laptop.- Recovery and analysis of long read metagenome-assembled genomes.- Cloud Computing for Metagenomics: Building a personalised computational platform forpipeline analyses.- Artificial Intelligence in Medicine: Microbiome-based Machine Learning for Phenotypic Classification.- Tracking Antibiotic Resistance From the Environment to Human Health.- Targeted enrichment of low-abundance and uncharacterised taxon members in complex microbial community with primer-free FISH probes.- Assembly and Annotation of Viral Metagenomes from Short-Read Sequencing Data.- Assembly and Annotation of Viral Metagenomes from Short-Read Sequencing Data.- Metagenomics Data Visualisation using R.- Comprehensive guideline for microbiome analysis using R packages.