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WHAM!: a web-based visualization suite for user-defined analysis of metagenomic shotgun sequencing data
- Source :
- BMC Genomics, BMC Genomics, Vol 19, Iss 1, Pp 1-11 (2018)
- Publication Year :
- 2018
- Publisher :
- Springer Science and Business Media LLC, 2018.
-
Abstract
- Background Exploration 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. Results We 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. Conclusions WHAM! 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 material The online version of this article (10.1186/s12864-018-4870-z) contains supplementary material, which is available to authorized users.
- Subjects :
- 0301 basic medicine
lcsh:QH426-470
Data exploration
Interface (Java)
lcsh:Biotechnology
Biology
Expression analysis
RShiny
03 medical and health sciences
0302 clinical medicine
Data visualization
lcsh:TP248.13-248.65
Genetics
Interactive visualization
Shotgun sequencing
business.industry
Command-line interface
Microbiota
Suite
Computational Biology
High-Throughput Nucleotide Sequencing
Data science
lcsh:Genetics
030104 developmental biology
Workflow
Metagenomics
Microbiome
DNA analysis
Metatranscriptomic
business
Software
030217 neurology & neurosurgery
Biotechnology
Subjects
Details
- ISSN :
- 14712164
- Volume :
- 19
- Database :
- OpenAIRE
- Journal :
- BMC Genomics
- Accession number :
- edsair.doi.dedup.....79769bc1f62af09598423c20f7351d5d