Phyloseq

Denoising Amplicon Sequence Data Using USEARCH and UNOISE3

During the Introduction to Metagenomics Summer Workshop we discussed denoising amplicon sequence variants and worked through Ben Callahan’s DADA2 tutorial. During that session, I mentioned several other approaches and algorithms for denoising or clustering amplicon sequence data including UNOISE3, DeBlur and Mothur. I also mentioned I would try to post some example workflows for some of these other approaches to highlight the similarities, as well as the differences. It looks like I am just now getting around to it.

Introduction to Phyloseq

This post is from a tutorial demonstrating the processing of amplicon short read data in R taught as part of the Introduction to Metagenomics Summer Workshop. It provides a quick introduction some of the functionality provided by phyloseq and follows some of Paul McMurdie’s excellent tutorials. This tutorial picks up where Ben Callahan’s DADA2 tutorial leaves off and highlights some of the main accessor and processor functions of the package.

Introduction to Microbiome Data Analysis

This was a talk given as part of the UC-CCHMC introductory workshop covering the basics of microbial metagenomic sequence data processing and statistical analysis. Topics covered in this talk include an introduction to challenging features of …

Introduction to Denoising Amplicon Sequence Data in R

This was a talk given as part of the UC-CCHMC introductory workshop covering the basics of microbial metagenomic sequence data processing and statistical analysis. Topics covered include an introduction to denoising 16S rRNA gene sequencing data, a …