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EzMAP: Easy Microbiome Analysis Platform
DC Field | Value | Language |
---|---|---|
dc.contributor.author | Shanmugam, Gnanendra | - |
dc.contributor.author | Lee, Song Hee | - |
dc.contributor.author | Jeon, Junhyun | - |
dc.date.accessioned | 2021-06-28T01:51:49Z | - |
dc.date.available | 2021-06-28T10:59:33Z | - |
dc.date.issued | 2021-04-07 | - |
dc.identifier.citation | BMC Bioinformatics. 2021 Apr 07;22(1):179 | ko_KR |
dc.identifier.issn | 1471-2105 | - |
dc.identifier.uri | https://hdl.handle.net/10371/174631 | - |
dc.description.abstract | Background
The rapid advances in next-generation sequencing technologies have revolutionized the microbiome research by greatly increasing our ability to understand diversity of microbes in a given sample. Over the past decade, several computational pipelines have been developed to efficiently process and annotate these microbiome data. However, most of these pipelines require an implementation of additional tools for downstream analyses as well as advanced programming skills. Results Here we introduce a user-friendly microbiome analysis platform, EzMAP (Easy Microbiome Analysis Platform), which was developed using Java Swings, Java Script and R programming language. EzMAP is a standalone package providing graphical user interface, enabling easy access to all the functionalities of QIIME2 (Quantitative Insights Into Microbial Ecology) as well as streamlined downstream analyses using QIIME2 output as input. This platform is designed to give users the detailed reports and the intermediate output files that are generated progressively. The users are allowed to download the features/OTU table (.biom;.tsv;.xls), representative sequences (.fasta) and phylogenetic tree (.nwk), taxonomy assignment file (optional). For downstream analyses, users are allowed to perform relative abundances (at all taxonomical levels), community comparison (alpha and beta diversity, core microbiome), differential abundances (DESeq2 and linear discriminant analysis) and functional prediction (PICRust, Tax4Fun and FunGuilds). Our case study using a published rice microbiome dataset demonstrates intuitive user interface and great accessibility of the EzMAP. Conclusions This EzMAP allows users to consolidate the microbiome analysis processes from raw sequence processing to downstream analyses specific for individual projects. We believe that this will be an invaluable tool for the beginners in their microbiome data analysis. This platform is freely available at https://github.com/gnanibioinfo/EzMAP and will be continually updated for adoption of changes in methods and approaches. | ko_KR |
dc.description.sponsorship | This work was supported by grants from Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, and Forestry through Agricultural Microbiome R&D Program, funded by Ministry of Agriculture, Food, and Rural Afairs (MAFRA) (918017–04), by a grant from Rural Development Administration (PJ013178), and by a grant from National Research Foundation of Korea (NRF-2018R1A5A1023599). The funding bodies were not involved in the design of EzMAP and, analysis of data, and in writing the manuscript. | ko_KR |
dc.language.iso | en | ko_KR |
dc.publisher | BMC | ko_KR |
dc.subject | Microbiome analysis platform | - |
dc.subject | Microbiome data analysis | - |
dc.subject | QIIME2 analysis | - |
dc.subject | Microbiome user-friendly tool | - |
dc.subject | Microbiome data visualization | - |
dc.title | EzMAP: Easy Microbiome Analysis Platform | ko_KR |
dc.type | Article | ko_KR |
dc.contributor.AlternativeAuthor | 이송희 | - |
dc.contributor.AlternativeAuthor | 전준현 | - |
dc.identifier.doi | doi.org/10.1186/s12859-021-04106-7 | - |
dc.citation.journaltitle | BMC Bioinformatics | ko_KR |
dc.language.rfc3066 | en | - |
dc.rights.holder | The Author(s) | - |
dc.date.updated | 2021-04-12T08:05:33Z | - |
dc.citation.number | 1 | ko_KR |
dc.citation.startpage | 179 | ko_KR |
dc.citation.volume | 22 | ko_KR |
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