iMAP: An integrated bioinformatics and visualization pipeline for microbiome data analysis
One of the major challenges facing investigators in the microbiome field is turning large numbers of reads generated by next-generation sequencing (NGS) platforms into biological knowledge. Effective analytical workflows that guarantee reproducibility, repeatability, and result provenance are essent...
| Autores principales: | , , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Springer
2019
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/106339 |
| _version_ | 1855524785012867072 |
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| author | Buza, T.M. Tonui, Triza Stomeo, Francesca Tiambo, Christian K. Katani, R. Schilling, M. Lyimo, B. Gwakisa, P.S. Cattadori, I.M. Buza, J. Kapur, V. |
| author_browse | Buza, J. Buza, T.M. Cattadori, I.M. Gwakisa, P.S. Kapur, V. Katani, R. Lyimo, B. Schilling, M. Stomeo, Francesca Tiambo, Christian K. Tonui, Triza |
| author_facet | Buza, T.M. Tonui, Triza Stomeo, Francesca Tiambo, Christian K. Katani, R. Schilling, M. Lyimo, B. Gwakisa, P.S. Cattadori, I.M. Buza, J. Kapur, V. |
| author_sort | Buza, T.M. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | One of the major challenges facing investigators in the microbiome field is turning large numbers of reads generated by next-generation sequencing (NGS) platforms into biological knowledge. Effective analytical workflows that guarantee reproducibility, repeatability, and result provenance are essential requirements of modern microbiome research. For nearly a decade, several state-of-the-art bioinformatics tools have been developed for understanding microbial communities living in a given sample. However, most of these tools are built with many functions that require an in-depth understanding of their implementation and the choice of additional tools for visualizing the final output. Furthermore, microbiome analysis can be time-consuming and may even require more advanced programming skills which some investigators may be lacking.We have developed a wrapper named iMAP (Integrated Microbiome Analysis Pipeline) to provide the microbiome research community with a user-friendly and portable tool that integrates bioinformatics analysis and data visualization. The iMAP tool wraps functionalities for metadata profiling, quality control of reads, sequence processing and classification, and diversity analysis of operational taxonomic units. This pipeline is also capable of generating web-based progress reports for enhancing an approach referred to as review-as-you-go (RAYG). For the most part, the profiling of microbial community is done using functionalities implemented in Mothur or QIIME2 platform. Also, it uses different R packages for graphics and R-markdown for generating progress reports. We have used a case study to demonstrate the application of the iMAP pipeline.The iMAP pipeline integrates several functionalities for better identification of microbial communities present in a given sample. The pipeline performs in-depth quality control that guarantees high-quality results and accurate conclusions. The vibrant visuals produced by the pipeline facilitate a better understanding of the complex and multidimensional microbiome data. The integrated RAYG approach enables the generation of web-based reports, which provides the investigators with the intermediate output that can be reviewed progressively. The intensively analyzed case study set a model for microbiome data analysis. |
| format | Journal Article |
| id | CGSpace106339 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2019 |
| publishDateRange | 2019 |
| publishDateSort | 2019 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1063392025-12-08T10:11:39Z iMAP: An integrated bioinformatics and visualization pipeline for microbiome data analysis Buza, T.M. Tonui, Triza Stomeo, Francesca Tiambo, Christian K. Katani, R. Schilling, M. Lyimo, B. Gwakisa, P.S. Cattadori, I.M. Buza, J. Kapur, V. bioinformatics data phylogeny research data analysis One of the major challenges facing investigators in the microbiome field is turning large numbers of reads generated by next-generation sequencing (NGS) platforms into biological knowledge. Effective analytical workflows that guarantee reproducibility, repeatability, and result provenance are essential requirements of modern microbiome research. For nearly a decade, several state-of-the-art bioinformatics tools have been developed for understanding microbial communities living in a given sample. However, most of these tools are built with many functions that require an in-depth understanding of their implementation and the choice of additional tools for visualizing the final output. Furthermore, microbiome analysis can be time-consuming and may even require more advanced programming skills which some investigators may be lacking.We have developed a wrapper named iMAP (Integrated Microbiome Analysis Pipeline) to provide the microbiome research community with a user-friendly and portable tool that integrates bioinformatics analysis and data visualization. The iMAP tool wraps functionalities for metadata profiling, quality control of reads, sequence processing and classification, and diversity analysis of operational taxonomic units. This pipeline is also capable of generating web-based progress reports for enhancing an approach referred to as review-as-you-go (RAYG). For the most part, the profiling of microbial community is done using functionalities implemented in Mothur or QIIME2 platform. Also, it uses different R packages for graphics and R-markdown for generating progress reports. We have used a case study to demonstrate the application of the iMAP pipeline.The iMAP pipeline integrates several functionalities for better identification of microbial communities present in a given sample. The pipeline performs in-depth quality control that guarantees high-quality results and accurate conclusions. The vibrant visuals produced by the pipeline facilitate a better understanding of the complex and multidimensional microbiome data. The integrated RAYG approach enables the generation of web-based reports, which provides the investigators with the intermediate output that can be reviewed progressively. The intensively analyzed case study set a model for microbiome data analysis. 2019-12 2019-12-26T11:27:53Z 2019-12-26T11:27:53Z Journal Article https://hdl.handle.net/10568/106339 en Open Access Springer Buza, T.M., Tonui, T., Stomeo, F., Tiambo, C., Katani, R., Schilling, M., Lyimo, B., Gwakisa, P., Cattadori, I.M., Buza, J. and Kapur, V. 2019. iMAP: An integrated bioinformatics and visualization pipeline for microbiome data analysis. BMC Bioinformatics 20: 374 |
| spellingShingle | bioinformatics data phylogeny research data analysis Buza, T.M. Tonui, Triza Stomeo, Francesca Tiambo, Christian K. Katani, R. Schilling, M. Lyimo, B. Gwakisa, P.S. Cattadori, I.M. Buza, J. Kapur, V. iMAP: An integrated bioinformatics and visualization pipeline for microbiome data analysis |
| title | iMAP: An integrated bioinformatics and visualization pipeline for microbiome data analysis |
| title_full | iMAP: An integrated bioinformatics and visualization pipeline for microbiome data analysis |
| title_fullStr | iMAP: An integrated bioinformatics and visualization pipeline for microbiome data analysis |
| title_full_unstemmed | iMAP: An integrated bioinformatics and visualization pipeline for microbiome data analysis |
| title_short | iMAP: An integrated bioinformatics and visualization pipeline for microbiome data analysis |
| title_sort | imap an integrated bioinformatics and visualization pipeline for microbiome data analysis |
| topic | bioinformatics data phylogeny research data analysis |
| url | https://hdl.handle.net/10568/106339 |
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