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Meet the New 16S Metagenomics App

Chris Probert and Ilya Chorny, Ph.D.
| May 19, 2014

BaseSpace 16S metagenomicsWe are pleased to announce the release of Illumina’s 16S Metagenomics app in BaseSpace. This app is an extension of the metagenomics workflow found in the MiSeq Reporter Software (MSR) 2.3 and 2.4. The 16S Metagenomics app provides ultra-fast taxonomic classification of the bacterial 16S rRNA gene without the need for upfront OTU clustering. The reads are classified against the GreenGenes database, with species-level sensitivity. The classification algorithm is based on a high-performance implementation of the RDP naïve Bayesian algorithm. The app takes advantage of Illumina paired-end sequencing, which enables researchers to classify longer regions of the 16S rRNA gene, such as V3-V4 region, as described in Illumina’s 16S demonstrated protocol , resulting in improved classification sensitivity.

Like other Illumina apps where the focus has been on accessibility, the 16S app offers highly interactive visualizations to explore taxonomic classification results. A sunburst chart allows viewing both taxonomic hierarchy and relative abundance of classifications in one figure.

BaseSpace 16S metagenomics sunburst classifcation chart

When viewed in a browser, a tooltip provides labels for each category, and the user can select a part of the graph to re-render the chart with that category at the root – allowing users to better explore categories of particular interest. The app also displays a bar chart showing the breakdown of taxonomic classifications at each level.

The app has additional features not found in MSR, such as aggregate analysis between multiple samples. This includes a Principal Coordinate Analysis (PCoA) that shows how similar/different each sample is to each other when compared to a user-adjustable level of taxonomy classification. Additionally, the app shows an interactive hierarchical dendrogram of the samples, which shows how samples are clustered when compared at Genus-level classifications.

BaseSpace 16S metagenomic hierarchical clustering dendogram

The interactive features of the app provide insight into the taxonomic composition of the samples. Users can both explore diversity on a per-sample basis through the sunburst chart and bar charts, and also gain insights into the differences between their samples through the PCoA and dendrogram charts.

Summarized classification statistics for both per-sample and aggregate analysis are available in the output files section as .CSV files that open easily in spreadsheet viewing software. Raw classification output (including classification confidence measures) are also available in the output files section for users wishing to perform further analysis.

A detailed user guide that describes the underlying methods in the application and how to access and run the app in BaseSpace is available. Publicly available data can be accessed and used to test drive the app.