Mitra Suparna (ed.) Metagenomic Data Analysis

Humana Press, 2023. — 443 p. — (Methods in Molecular Biology 2649). — ISBN 978-1-0716-3071-6.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 using most 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 Personalized Computational Platform for Pipeline 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 Uncharacterized Taxon Members in Complex Microbial Community with Primer-Free FISH Probes Designed from Next Generation Sequencing Dataset
Assembly and Annotation of Viral Metagenomes from Short-Read Sequencing Data
Manipulating and Basic Analysis of Tabular Metagenomics Datasets Using R
Metagenomics Data Visualization Using R