January 17, 2023: Metabarcoding: a soup to nuts workshop exploring the basic methods of analysis

Workshop presented by: NH-INBRE, CIBBR, NHAES, & The Hubbard Center for Genome Studies (HCGS)
When: Tuesday, January 17th 12:30-3:00 pm and Wednesday, January 18th 9:00-3:00 PM
Where: In-person and online. Gregg Hall, room TBD
Speakers:  Joseph Sevigny, HCGS
                   Lawrence Gordon, HCGS
Kelley Thomas, Director of HCGS

Please email joseph.sevigny@unh.edu by January 15th to sign up.

Zoom Link: https://unh.zoom.us/j/96313262064

Workshop Summary:
This two-day workshop is intended for students/staff who are new to genomic and bioinformatic applications. Here we focus on metabarcoding, which is the use of a limited number of phylogenetically and taxonomically informative DNA sequences to identify species in complex communities.  This technique is foundational to major areas of research including microbiome and environmental DNA (eDNA) analysis. This workshop will briefly walk through the generation of data (via amplicon sequencing) followed by in-depth hands-on analysis including evaluation of data quality, identification of the unique sequence variants, analysis of standard diversity metrics and visualizations. This workshop utilizes the popular QIIME II platform.

Topics to include:

  1. Introduction to Next Generation Sequencing (NGS)
  2. Discussion of amplicon/microbiome analysis
  3. BASH and the command-line environment
  4. Guided bioinformatic workflow in QIIME2
    1. Importing data and quality control
    2. Denoising and construction of ASV tables
    3. Taxonomic classification of sequences
    4. Beta and alpha diversity analyses
    5. Data visualizations, reporting, submission of data
    6. Rigor and reproducibility in bioinformatics