Below I provide scripts to implement several workflows for denoising 16s rRNA gene sequences used by the Microbial Metagenomics Analysis Center (MMAC) at CCHMC for paired-end data. These scripts are written to run on the CCHMC high-performance computing (HPC) cluster.
Below I provide scripts to implement the current default workflow for taxonomic profiling using Kraken2 and Bracken and functional profiling using HUMAnN2 used by the Microbial Metagenomics Analysis Center (MMAC) at CCHMC for paired-end data.
I recently read through Calgaro et. al. “Assessment of statistical methods from single cell, bulk RNA-seq, and metagenomics applied to microbiome data” where they examined the performance of statistical models developed for bulk RNA (RNA-seq), single-cell RNA-seq (scRNA-seq), and microbial metagenomics to:
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.
A collaborator recently asked if I could help pull down a few thousand sequence files from the NCBI Sequence Read Archive (SRA) for a secondary analysis. This is a short post primarily to help me (and hopefully others) remember how to do this once you have a set of SRR IDs of interest.
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 post is also from the Introduction to Metagenomics Summer Workshop and provides a quick introduction to some common analytic methods used to analyze microbiome data. I thought it might be of interest to a broader audience so decided to post it here.
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 …
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 …
These slides are from an invited talk I gave to the Division of Gastroenterology, Hepatology and Nutrition at CCHMC as part of their Digestive Health Center Seminar Series. Topics covered in this talk include an introduction to denoising amplicon …