IMPLEMENTATION OF KRONA INTO QIIME 2

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2022-5-9

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Büyükaltay, Kaan

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Microbiome studies mainly use two different approaches: metagenomic and amplicon analysis. The metagenomic analysis is based on a whole-genome shotgun approach. It is possible to acquire taxonomic resolution to species and strain level but requires high computational power and is expensive. In the amplicon analysis approach, marker genes like 16S, 18S, and ITS are used to identify the sequences. These genes are highly conserved but contain hypervariable regions, allowing researchers to acquire taxonomic resolution at the genus level. The downside of this approach is due to the biases introduced with PCR and its high error rate. QIIME 2 is a tool consisting of many plugins for amplicon analysis. QIIME 2 team has a decentralized development approach so that third parties can develop new plugins and share them with the community. Although there are different options for visualizations in QIIME 2, there is no tool for visualizing the contents of the features table for a single sample. On the other hand, Krona is a tool that visualizes hierarchical data as multi-layered pie charts. While this visualization is desired, it is not a straightforward task, as the QIIME 2 and Krona do not share the same data formats. This study aims to fill this gap by developing a plugin that will transfer QIIME2 outputs into Krona to ease the visualization of QIIME 2 analysis results with Krona without additional script or manipulation during amplicon analysis.

Subject Keywords

metagenome, amplicon, plugin development

URI

https://hdl.handle.net/11511/97889

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Graduate School of Informatics, Thesis

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Citation Formats

K. Büyükaltay, “IMPLEMENTATION OF KRONA INTO QIIME 2,” M.S. - Master of Science, Middle East Technical University, 2022.