The DOI matches its Crossref record; 29 of the 29 references it cites were found in a registry or an index.
A practical guide to amplicon and metagenomic analysis of microbiome data
Open accessAbstract
Advances in high-throughput sequencing (HTS) have fostered rapid developments in the field of microbiome research, and massive microbiome datasets are now being generated. However, the diversity of software tools and the complexity of analysis pipelines make it difficult to access this field. Here, we systematically summarize the advantages and limitations of microbiome methods. Then, we recommend specific pipelines for amplicon and metagenomic analyses, and describe commonly-used software and databases, to help researchers select the appropriate tools. Furthermore, we introduce statistical and visualization methods suitable for microbiome analysis, including alpha- and beta-diversity, taxonomic composition, difference comparisons, correlation, networks, machine learning, evolution, source tracing, and common visualization styles to help researchers make informed choices. Finally, a step-by-step reproducible analysis guide is introduced. We hope this review will allow researchers to carry out data analysis more effectively and to quickly select the appropriate tools in order to efficiently mine the biological significance behind the data.
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Cites
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Self-citationSalmon provides fast and bias-aware quantification of transcript expression
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Tumor-resident intracellular microbiota promotes metastatic colonization in breast cancer
Fu, A., Yao, B., Dong, T., Chen, Y., Yao, J., Liu, Y., Li, H., Bai, H., Liu, X., Zhang, Y., et al. (2022) · Cell · doi:10.1016/j.cell.2022.02.027 · Cited by 981
Self-citationThe Role of Microbiota-Gut-Brain Axis in Neuropsychiatric and Neurological Disorders
Socała, K., Doboszewska, U., Szopa, A., Serefko, A., Włodarczyk, M., Zielińska, A., Poleszak, E., Fichna, J., & Wlaź, P. (2021) · Pharmacological Research · doi:10.1016/j.phrs.2021.105840 · Cited by 857
Next-generation sequencing: insights to advance clinical investigations of the microbiome
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Understanding the gut microbiota and sarcopenia: a systematic review
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The best practice for microbiome analysis using R
Wen, T., Niu, G., Chen, T., Shen, Q., Yuan, J., & Liu, Y.-X. (2023) · Protein & Cell · doi:10.1093/procel/pwad024 · Cited by 139
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Metadata
- Authors
- Liu, Y.-X., Qin, Y., Chen, T., Lu, M., Qian, X., Guo, X., & Bai, Y.
- Venue
- Protein & Cell
- Publisher
- Oxford University Press (OUP)
- Published
- 2020-05-11
- Volume
- 12
- Issue
- 5
- Pages
- 315-330
- ISSN
- 1674-800X (ISSN-L)
- 1674-8018
- OpenAlex
- W3024376490
- Cited by
- 864
- References
- 29
- FWCI
- 27.59
- Type
- journal article
- Language
- en
- Open access
- gold
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