iMAP: An integrated bioinformatics and visualization pipeline for microbiome data analysis

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cg.authorship.typesCGIAR and developing country institute
cg.authorship.typesCGIAR and advanced research institute
cg.contributor.affiliationPennsylvania State University
cg.contributor.affiliationInternational Livestock Research Institute
cg.contributor.affiliationNelson Mandela Africa Institution of Science and Technology
cg.contributor.affiliationSokoine University of Agriculture
cg.contributor.affiliationEuropean Molecular Biology Laboratory
cg.contributor.donorUnited States Defense Threat Reduction Agency
cg.creator.identifierChristian Keambou Tiambo: 0000-0002-7401-753X
cg.howPublishedFormally Published
cg.identifier.doihttps://doi.org/10.1186/s12859-019-2965-4
cg.isijournalISI Journal
cg.issn1471-2105
cg.issue1
cg.journalBMC Bioinformatics
cg.number374
cg.reviewStatusPeer Review
cg.subject.ilriBIOTECHNOLOGY
cg.subject.ilriDATA
cg.subject.ilriRESEARCH
cg.volume20
dc.contributor.authorBuza, T.M.
dc.contributor.authorTonui, Triza
dc.contributor.authorStomeo, Francesca
dc.contributor.authorTiambo, Christian K.
dc.contributor.authorKatani, R.
dc.contributor.authorSchilling, M.
dc.contributor.authorLyimo, B.
dc.contributor.authorGwakisa, P.S.
dc.contributor.authorCattadori, I.M.
dc.contributor.authorBuza, J.
dc.contributor.authorKapur, V.
dc.date.accessioned2019-12-26T11:27:53Zen
dc.date.available2019-12-26T11:27:53Zen
dc.identifier.urihttps://hdl.handle.net/10568/106339
dc.titleiMAP: An integrated bioinformatics and visualization pipeline for microbiome data analysisen
dcterms.abstractOne 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.en
dcterms.accessRightsOpen Access
dcterms.audienceScientists
dcterms.available2019-07-03
dcterms.bibliographicCitationBuza, 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: 374en
dcterms.issued2019-12
dcterms.languageen
dcterms.licenseCC-BY-4.0
dcterms.publisherSpringer
dcterms.subjectbioinformaticsen
dcterms.subjectdataen
dcterms.subjectphylogenyen
dcterms.subjectresearchen
dcterms.subjectdata analysisen
dcterms.typeJournal Article

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