A review of common methods used in the analysis of human microbiome sequencing data [version 1; peer review: awaiting peer review]

The past two decades have seen a rapid rise in the development and use of sequencing technologies. The advent of high-throughput sequencing (HTS) has allowed scientists to sequence the genomic content of entire microbial communities rapidly and affordably. Methods for data management, visualization,...

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Bibliographic Details
Published in:F1000 research 2024, Vol.13, p.369
Main Authors: Hannan, Patrick, Nicol, Mark, Lesosky, Maia
Format: Article
Language:English
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Summary:The past two decades have seen a rapid rise in the development and use of sequencing technologies. The advent of high-throughput sequencing (HTS) has allowed scientists to sequence the genomic content of entire microbial communities rapidly and affordably. Methods for data management, visualization, and analysis of this microbiome sequencing data are now widespread in open and closed source software tools. In this review, we identify common analysis methods used in microbiome sequencing studies, including methods for normalisation of abundance table data, visualization of high-dimensional microbiome data and the analysis of longitudinal microbiome sequencing data. In particular we find that a very small proportion of metagenomic studies made use of compositional data analysis methods and none that made use of compositional methods for longitudinal microbiome data.
ISSN:2046-1402
2046-1402
DOI:10.12688/f1000research.110605.1