16s-seq

Materials and presentation for the 2022 ISB Microbiome course.

Materials and presentation for the 2023 ISB Microbiome course.

A Qiime plugin for MICOM.

RAPID - R based Amplicon Pipeline for Interactive DADA2 - A unified Shiny application that takes you from raw amplicon data to ASV and taxonomy tables with DADA2, and onward to ecology visualizations, PERMANOVA, and ANCOM-BC2 analyses.

MicrobiomeStat Tutorial Repository: This is a comprehensive resource for learning how to use the MicrobiomeStat package. It provides a step-by-step guide to effectively analyze complex microbiome data.

Quantitative metagenomic alignment and taxonomic exact-matching

A quick and user-friendly pipeline to go from raw fastq data from Illumina (paired-end sequencing) to processed ASVs and Taxonomic data.

A tool to identify and extract the commonly used ITS folding motifs from a 16s-23s rRNA sequence.

LotuS version 3

16S SNAPP on Python 3 - version 2

VSEARCH pipeline for ASV inference of 16S seq data

Metagenomic, metatranscriptomic, and 16S rRNA gene marker analyses of seawater and sea-ice samples from spill simulations performed at the Churchill Marine Observatory (Churchill, Manitoba, Canada). This repository includes work from 2 experiments: Nov2024-Jan2025 and Nov-2025-June2026

SPIEC-EASI Network Modeling of Bacterial Communities (TwinsUK).

This repository contains my first analysis workflow using Qiita and Qiime 2. It processes and analyses 16s rRNA data from my raw reads for diversity analysis and taxonomy

Analysis of cyanobacteria 16S eDNA sequences obtained from stormwater management ponds using QIIME 2 and R.

The structure of total and viable microbial communities from the atmosphere was monitored during a small snowfall event in the University of Guelph Arboretum. We sought to understand the impact of snowfall to shape the aeromicrobiome alongside influences from surrounding surface environments.

Code associated with the following manuscript, currently in review: M.S. Fischer, N.J. Patel, P.J. De Lorimier, M.F. Traxler "Prescribed fire selects for a pyrophilous soil subcommunity in a northern California mixed conifer forest"

A R script for the study of the prokaryotic community of the sponge Dactylospongia metachromia

Workflow of community composition and diversity analyses of bacteria and archaea with QIIME 2

AU microbiome molecular exploratory analyses for NSW