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

One of the major challenges facing investigators in the microbiomefield 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 microbiomeresearch. For nearly a decade, several state-of-the-art bioinformatics tools have been developed for understanding microbial communities livingin 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, microbiomeanalysis 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 MicrobiomeAnalysis Pipeline) to provide the microbiomeresearch community with a user-friendly and portable tool that integrates bioinformaticsanalysis 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 Mothuror QIIME2 platform. Also, it uses different R packages for graphics and R- markdownfor 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 microbiomedata. 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 microbiomedata analysis.