iVikodak—A Platform and Standard Workflow for Inferring, Analyzing, Comparing, and Visualizing the Functional Potential of Microbial Communities
Background: The objectives of any metagenomic study typically include identification of resident microbes and their relative proportions (taxonomic analysis), profiling functional diversity (functional analysis), and comparing the identified microbes and functions with available metadata (comparativ...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2019-01-01
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| Series: | Frontiers in Microbiology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/article/10.3389/fmicb.2018.03336/full |
| _version_ | 1819103185185275904 |
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| author | Sunil Nagpal Mohammed Monzoorul Haque Rashmi Singh Sharmila S. Mande |
| author_facet | Sunil Nagpal Mohammed Monzoorul Haque Rashmi Singh Sharmila S. Mande |
| author_sort | Sunil Nagpal |
| collection | DOAJ |
| description | Background: The objectives of any metagenomic study typically include identification of resident microbes and their relative proportions (taxonomic analysis), profiling functional diversity (functional analysis), and comparing the identified microbes and functions with available metadata (comparative metagenomics). Given the advantage of cost-effectiveness and convenient data-size, amplicon-based sequencing has remained the technology of choice for exploring phylogenetic diversity of an environment. A recent school of thought, employing the existing genome annotation information for inferring functional capacity of an identified microbiome community, has given a promising alternative to Whole Genome Shotgun sequencing for functional analysis. Although a handful of tools are currently available for function inference, their scope, functionality and utility has essentially remained limited. Need for a comprehensive framework that expands upon the existing scope and enables a standardized workflow for function inference, analysis, and visualization, is therefore felt.Methods: We present iVikodak, a multi-modular web-platform that hosts a logically inter-connected repertoire of functional inference and analysis tools, coupled with a comprehensive visualization interface. iVikodak is equipped with microbial co-inhabitance pattern driven published algorithms along with multiple updated databases of various curated microbe-function maps. It also features an advanced task management and result sharing system through introduction of personalized and portable dashboards.Results: In addition to inferring functions from 16S rRNA gene data, iVikodak enables (a) an in-depth analysis of specific functions of interest (b) identification of microbes contributing to various functions (c) microbial interaction patterns through function-driven correlation networks, and (d) simultaneous functional comparison between multiple microbial communities. We have bench-marked iVikodak through multiple case studies and comparisons with existing state of art. We also introduce the concept of a public repository which provides a first of its kind community-driven framework for scientific data analytics, collaboration and sharing in this area of microbiome research.Conclusion: Developed using modern design and task management practices, iVikodak provides a multi-modular, yet inter-operable, one-stop framework, that intends to simplify the entire approach toward inferred function analysis. It is anticipated to serve as a significant value addition to the existing space of functional metagenomics.iVikodak web-server may be freely accessed at https://web.rniapps.net/iVikodak/. |
| first_indexed | 2024-12-22T01:46:26Z |
| format | Article |
| id | doaj.art-f017058d414a48f2941c5aa5915231ad |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-22T01:46:26Z |
| publishDate | 2019-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-f017058d414a48f2941c5aa5915231ad2022-12-21T18:43:04ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2019-01-01910.3389/fmicb.2018.03336429477iVikodak—A Platform and Standard Workflow for Inferring, Analyzing, Comparing, and Visualizing the Functional Potential of Microbial CommunitiesSunil NagpalMohammed Monzoorul HaqueRashmi SinghSharmila S. MandeBackground: The objectives of any metagenomic study typically include identification of resident microbes and their relative proportions (taxonomic analysis), profiling functional diversity (functional analysis), and comparing the identified microbes and functions with available metadata (comparative metagenomics). Given the advantage of cost-effectiveness and convenient data-size, amplicon-based sequencing has remained the technology of choice for exploring phylogenetic diversity of an environment. A recent school of thought, employing the existing genome annotation information for inferring functional capacity of an identified microbiome community, has given a promising alternative to Whole Genome Shotgun sequencing for functional analysis. Although a handful of tools are currently available for function inference, their scope, functionality and utility has essentially remained limited. Need for a comprehensive framework that expands upon the existing scope and enables a standardized workflow for function inference, analysis, and visualization, is therefore felt.Methods: We present iVikodak, a multi-modular web-platform that hosts a logically inter-connected repertoire of functional inference and analysis tools, coupled with a comprehensive visualization interface. iVikodak is equipped with microbial co-inhabitance pattern driven published algorithms along with multiple updated databases of various curated microbe-function maps. It also features an advanced task management and result sharing system through introduction of personalized and portable dashboards.Results: In addition to inferring functions from 16S rRNA gene data, iVikodak enables (a) an in-depth analysis of specific functions of interest (b) identification of microbes contributing to various functions (c) microbial interaction patterns through function-driven correlation networks, and (d) simultaneous functional comparison between multiple microbial communities. We have bench-marked iVikodak through multiple case studies and comparisons with existing state of art. We also introduce the concept of a public repository which provides a first of its kind community-driven framework for scientific data analytics, collaboration and sharing in this area of microbiome research.Conclusion: Developed using modern design and task management practices, iVikodak provides a multi-modular, yet inter-operable, one-stop framework, that intends to simplify the entire approach toward inferred function analysis. It is anticipated to serve as a significant value addition to the existing space of functional metagenomics.iVikodak web-server may be freely accessed at https://web.rniapps.net/iVikodak/.https://www.frontiersin.org/article/10.3389/fmicb.2018.03336/fullinferred functions16S metagenomefunctional metagenomicsfunctions of microbial communitiesmicrobiome analysisvisualization |
| spellingShingle | Sunil Nagpal Mohammed Monzoorul Haque Rashmi Singh Sharmila S. Mande iVikodak—A Platform and Standard Workflow for Inferring, Analyzing, Comparing, and Visualizing the Functional Potential of Microbial Communities Frontiers in Microbiology inferred functions 16S metagenome functional metagenomics functions of microbial communities microbiome analysis visualization |
| title | iVikodak—A Platform and Standard Workflow for Inferring, Analyzing, Comparing, and Visualizing the Functional Potential of Microbial Communities |
| title_full | iVikodak—A Platform and Standard Workflow for Inferring, Analyzing, Comparing, and Visualizing the Functional Potential of Microbial Communities |
| title_fullStr | iVikodak—A Platform and Standard Workflow for Inferring, Analyzing, Comparing, and Visualizing the Functional Potential of Microbial Communities |
| title_full_unstemmed | iVikodak—A Platform and Standard Workflow for Inferring, Analyzing, Comparing, and Visualizing the Functional Potential of Microbial Communities |
| title_short | iVikodak—A Platform and Standard Workflow for Inferring, Analyzing, Comparing, and Visualizing the Functional Potential of Microbial Communities |
| title_sort | ivikodak a platform and standard workflow for inferring analyzing comparing and visualizing the functional potential of microbial communities |
| topic | inferred functions 16S metagenome functional metagenomics functions of microbial communities microbiome analysis visualization |
| url | https://www.frontiersin.org/article/10.3389/fmicb.2018.03336/full |
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