Abstract
Current microbiome applications require substantial bioinformatics expertise to execute. As microbiome clinical diagnostics are being developed, there is a critical need to implement computational tools and applications that are user-friendly for the medical community to understand microbiome correlation with the health. To address this need, we have developed BiomMiner (pronounced as “biominer”), an automated pipeline that provides a comprehensive analysis of microbiome data. The pipeline finds taxonomic signatures of microbiome data and compiles actionable clinical report that allows clinicians and biomedical scientists to efficiently perform statistical analysis and data mining on the large microbiome datasets. BiomMiner generates web-enabled visualization of the analysis results and is specifically designed to facilitate the use of microbiome datasets in clinical applications.
Highlights
Targeted amplicon-based analysis using 16S ribosomal RNA gene sequences is frequently used to explore complicated bacterial communities such as the human gut microbiome [1]
BiomMiner utilizes many publicly available tools to perform the major steps of 16S ribosomal RNA (rRNA) analysis
Other applications only focused on the downstream portion of the analysis and let the user upload their processed data which suffer from several issues like format incompatibility, unsupported annotation
Summary
Targeted amplicon-based analysis using 16S ribosomal RNA (rRNA) gene sequences is frequently used to explore complicated bacterial communities such as the human gut microbiome [1]. This approach has been used since 2007 for clinical diagnostics [2]. The most popular open source packages are QIIME [5] and mothur [6] Both QIIME and mother are all selfcontained pipelines which can be used to analyze 16S rRNA gene sequencing data. Due to their comprehensive features and support documentation, QIIME and mother are considered the standard applications for microbiome analysis [7, 8].
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