Abstract

BackgroundOne 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.ResultsWe 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.ConclusionsThe 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.

Highlights

  • 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

  • We used a case study to demonstrate the application of the Integrated Microbiome Analysis Pipeline (iMAP) pipeline and the exploratory visualization that provides an insight into the results

  • The iMAP pipeline is integrated with custom functions that generate reports progressively to facilitate RAYG, a new approach associated with the pipeline to enable the investigators to review the intermediate output graphically and correct any obvious errors that may lead to wrong or misleading conclusions

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Summary

Introduction

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. Several state-of-the-art bioinformatics tools have been developed for understanding microbial communities living in a given sample. 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. The choice of bioinformatics methodology used for analyzing any microbiome dataset from pre-processing of the reads through the final step of the analysis is a key factor for gaining high-quality biological knowledge. Finding suitable tools that complete the analysis of microbiome data can be time-consuming and may even require more high-level programming experiences which some users may be lacking.

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