Metagenomic data analysis
著者
書誌事項
Metagenomic data analysis
（Methods in molecular biology / John M. Walker, series editor, 2649）（Springer protocols）
Humana Press, c2023
- : hbk
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注記
Includes bibliographical references and index
内容説明・目次
内容説明
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.
目次
1. From genomics to metagenomics in the era of recent sequencing technologies
Saskia Benz and Suparna Mitra
2. Quality Control in Metagenomics Data
Abraham Gihawi, Ryan Cardenas, Rachel Hurst, and Daniel S. Brewer
3. Metagenomics Databases for Bacteria Dapeng Wang
4. Amplicon Sequencing Pipelines in Metagenomics Dapeng Wang
5. A practical guide to 16S rRNA microbiome analysis in musculoskeletal disorders
Rooney CM and Mitra S.
6. DIAMOND+MEGAN microbiome analysis Anupam Gautam, Wenhuan Zeng, and Daniel H. Huson
7. Interactive Web-based Services for Metagenomic Data Analysis and Comparisons
Nehal Adel Abdelsalam, Hajar El-Shora, and Mohamed El-Hadidi
8. Application of High Throughput Sequencing (HTS) to Enhance the Well-being of an Endangered Species (Malayan tapir): Characterization of Gut Microbiome using MG-RAST
Ramitha Arumugam,Prithivan Ravichandran, Swee Keong Yeap, Reuben Sunil Kumar Sharma, Shahrizim Bin Zulkifly, Donny Yawah, and Geetha Annavi
9. Designing knowledge-based bioremediation strategies using metagenomics
Niti B. Jadeja and Atya Kapley
10. Nanopore sequencing techniques - A comparison of the MinKNOW and the Alignator sequencers Sebastian Oeck, Alicia I Tuns, an Alexander Schramm
11. MAIRA: protein-based analysis of MinION reads on a laptop
Caner Bagc , Benjamin Albrecht, and Daniel H. Huson
12. Recovery and analysis of long read metagenome-assembled genomes
Krithika Arumugam, Irina Bessarab, Mindia A. S. Haryono, and Rohan B.H. Williams
13. Cloud Computing for Metagenomics: Building a personalised computational platform for pipeline analyses Martin Callaghan
14. Artificial Intelligence in Medicine: Microbiome-based Machine Learning for Phenotypic Classification
Xi Cheng and Bina Joe
15. Tracking Antibiotic Resistance From the Environment to Human Health
Eman Abdelrazik and Mohamed El-Hadidi
16. Targeted enrichment of low-abundance and uncharacterised taxon members in complex microbial community with primer-free FISH probes
Pui Yi Maria Yung, Shi Ming Tan
17. Assembly and Annotation of Viral Metagenomes from Short-Read Sequencing Data
Mihnea R. Mangalea, Kristopher Keift, Breck A. Duerkop, and Karthik Anantharaman
18. Assembly and Annotation of Viral Metagenomes from Short-Read Sequencing Data
Mihnea R. Mangalea, Kristopher Keift, Breck A. Duerkop, and Karthik Anantharaman
19. Metagenomics Data Visualisation using R
Alex Coleman, Anupam Bose, and Suparna Mitra
20. Comprehensive guideline for microbiome analysis using R packages
Joseph N Boctor, Mariam Oweda, and Mohamed El-Hadidi
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