Methods for The Metagenomic Data Visualization and Analysis

Sudarikov, Konstantin; Tyakht, Alexander; Alexeev, Dmitry

doi:10.21775/cimb.024.037

Cited by 34 publications

(28 citation statements)

References 34 publications

(36 reference statements)

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“…Stacked bar plots are able to efficiently represent the proportion of taxa present in each sample across many metagenomes and are commonly used in microbiome studies. Heatmaps are particularly useful in highlighting the taxa and gene abundance in a collection of samples or for taxa correlation plots, where other methods such as box or bar plots can become cumbersome [ 23 ].…”

Section: Methodsmentioning

confidence: 99%

WHAM!: a web-based visualization suite for user-defined analysis of metagenomic shotgun sequencing data

Devlin¹,

Battaglia

Ruggles

2018

BMC Genomics

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BackgroundExploration of large data sets, such as shotgun metagenomic sequence or expression data, by biomedical experts and medical professionals remains as a major bottleneck in the scientific discovery process. Although tools for this purpose exist for 16S ribosomal RNA sequencing analysis, there is a growing but still insufficient number of user-friendly interactive visualization workflows for easy data exploration and figure generation. The development of such platforms for this purpose is necessary to accelerate and streamline microbiome laboratory research.ResultsWe developed the Workflow Hub for Automated Metagenomic Exploration (WHAM!) as a web-based interactive tool capable of user-directed data visualization and statistical analysis of annotated shotgun metagenomic and metatranscriptomic data sets. WHAM! includes exploratory and hypothesis-based gene and taxa search modules for visualizing differences in microbial taxa and gene family expression across experimental groups, and for creating publication quality figures without the need for command line interface or in-house bioinformatics.ConclusionsWHAM! is an interactive and customizable tool for downstream metagenomic and metatranscriptomic analysis providing a user-friendly interface allowing for easy data exploration by microbiome and ecological experts to facilitate discovery in multi-dimensional and large-scale data sets.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4870-z) contains supplementary material, which is available to authorized users.

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Section: Methodsmentioning

confidence: 99%

WHAM!: a web-based visualization suite for user-defined analysis of metagenomic shotgun sequencing data

Devlin¹,

Battaglia

Ruggles

2018

BMC Genomics

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“…Metagenomics sequencing technologies make it possible to find new viruses from the angle of the genome. In a few short years, metagenomics research has penetrated into all areas of potential viral life, including ocean, soil, hot springs, human oral cavities and the gastrointestinal tract [4][5][6][7][8][9]. Surprisingly, in nearshore marine environments, 65%…”

Section: Introductionmentioning

confidence: 99%

Metagenomic Analysis of the Virome in Lung Tissues and Guts of Wild Mice

Yin

Chen

Zhao

et al. 2020

Preprint

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Background Mice, as host animals of a variety of pathogens, can spread 60 kinds of human diseases including more than ten families of viruses including Poxviridae, Herpesviridae, and so on. Methods In this study, lung tissues and gut samples of 7-week-old mice from outdoor environments were sequenced using metagenomics, and an abundance of virome information was acquired. Results A total of 82 families of mammalian viruses, plant viruses, insect viruses, and phages were detected. Among the top 10 most abundant families were the RNA viruses Orthomyxoviridae, Picornaviridae, Bunyaviridae, and Arenaviridae, the DNA virus Herpesviridae, the insect viruses Nodaviridae and Baculoviridae, the plant virus Tombusviridae, and the phage Myoviridae. Except for Myoviridae, whose abundance in guts was higher than in lung tissues, the abundance of viruses in the lung tissues and guts showed no significant difference. Conclusions The data obtained in this study provided an overview of the viral community present in these mice samples, revealing some mouse-associated viruses closely related to known human or animal pathogens. Strengthening our understanding of unclassified viruses in mice in the natural environment could provide scientific guidance for the prevention and control of new viral outbreaks that can spread via rodents.

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“…Visual and statistical exploration of important functions of microbiota (like antibiotic resistance [ 1 ] and dietary fiber catabolism [ 2 , 3 ]) is of particular importance in the global context of publicly collected data. Lower costs and increasing popularity make metagenomics further available to smaller companies and research facilities that often lack dedicated staff bioinformaticians that can perform manual statistical analysis and insight-providing visualization according to state-of-art guidelines [ 4 , 5 ]. In order to optimize the translation of metagenomic surveys’ results into biomedically important knowledge and advance the global progress in collaborative microbiota research, we developed Knomics-Biota, a web-service for metagenomic data analysis that allows users without advanced skills in bioinformatics and software development to turn their “raw” data into intuitive analytical reports.…”

Section: Introductionmentioning

confidence: 99%

Knomics-Biota - a system for exploratory analysis of human gut microbiota data

et al. 2018

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BackgroundMetagenomic surveys of human microbiota are becoming increasingly widespread in academic research as well as in food and pharmaceutical industries and clinical context. Intuitive tools for investigating experimental data are of high interest to researchers.ResultsKnomics-Biota is a web-based resource for exploratory analysis of human gut metagenomes. Users can generate and share analytical reports corresponding to common experimental schemes (like case-control study or paired comparison). Interactive visualizations and statistical analysis are provided in association with the external factors and in the context of thousands of publicly available datasets arranged into thematic collections. The web-service is available at https://biota.knomics.ru.ConclusionsKnomics-Biota web service is a comprehensive tool for interactive metagenomic data analysis.Electronic supplementary materialThe online version of this article (10.1186/s13040-018-0187-3) contains supplementary material, which is available to authorized users.

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Methods for The Metagenomic Data Visualization and Analysis

Cited by 34 publications

References 34 publications

WHAM!: a web-based visualization suite for user-defined analysis of metagenomic shotgun sequencing data

WHAM!: a web-based visualization suite for user-defined analysis of metagenomic shotgun sequencing data

Metagenomic Analysis of the Virome in Lung Tissues and Guts of Wild Mice

Knomics-Biota - a system for exploratory analysis of human gut microbiota data

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