My name is Rachael Lappan, and I am a PhD candidate at the University of Western Australia. The core of my PhD work is the Perth Otitis Media Microbiome (biOMe) study, where I work on the upper respiratory tract microbiome in children with recurrent acute otitis media (middle ear infections). The first stage of this research involved characterising the microbiome (by 16S rRNA gene sequencing) on samples from children with ear infections compared with samples from seemingly resistant healthy controls. The paper can be found here.

The purpose of this document is to neatly record all of my analyses on the 16S amplicon data in this study.

If any part of this document is useful to you, you have questions, or something can be improved, you can Tweet at me (@RachaelLappan) or email me.

I would like to thank Ghislaine Platell for helping me integrate UPARSE into my pipeline.

This document was created with Bookdown and is hosted on my GitHub through a private repository.

Please note that QIIME1 and the 97% OTU-based workflow has been superseded by ASVs (100% OTUs) and the QIIME2 workflow: my analysis here may guide your own but I would strongly recommend following the QIIME2 tutorials.