Welcome to Wildlife Genomics 3 workshop

Dive into the Wild World of Genomics and Metagenomics!

Join our interactive, hands-on workshop designed to equip you with cutting-edge tools and techniques in wildlife genomics and conservation biology. Whether you're curious about decoding genomes to inform population management or exploring biodiversity through environmental DNA, this course offers something for everyone passionate about wildlife research and genetics.

On one track, delve into the fundamentals of Population Genetics and next-generation sequencing (NGS) data analysis including Illumina and Oxford Nanopore technologies. You will gain practical experience in analyzing genomic data for applications such as wildlife censuses, measuring genetic diversity, fitness and combating illegal wildlife trafficking. With workflows adaptable to RAD-seq, amplicon-seq, and more, if you’ve got a reference genome, you’re ready to go!

Alternatively, explore how Metagenomics and eDNA are revolutionizing wildlife monitoring. Learn how to extract meaningful insights from soil, water, feces, or blood meal samples to detect elusive species, trace pathogen outbreaks, map microbial communities, and uncover predator–prey relationships. These non-invasive techniques are ideal for challenging environments and ethically sensitive studies, offering powerful tools for ecosystem management and health surveillance.

Whether you're a beginner or looking to expand your genomic toolkit, this workshop allows you to tailor your learning path—choose your focus or blend both worlds for a comprehensive understanding of modern wildlife genomics.

Workshop Objectives

🧬 Population Genomics Track

• Understand and process raw sequencing data (FASTQ format)
• Perform quality control and preprocessing
• Map reads to a reference genome
• Identify variants (SNPs and indels)
• Use filtered variants for basic population genetic analysis (PCA, Admixture, heterozygosity)

🧪 Metagenomics & eDNA Track

• Introduce participants to eDNA metabarcoding and shotgun metagenomics workflows
• Provide hands-on experience in field collection, DNA extraction, and library preparation
• Train participants in sequence quality control, taxonomic assignment, and diversity metrics
• Explore use cases in wildlife health, habitat quality assessment, and ecosystem monitoring

Take a look at our reproducible version of other workshops, available at: PoODL-CES Workshops

Instructors

Pre-requisites & Setup

• Access to a Unix/Linux shell environment:
  • Windows: Install MobaXterm
  • Mac/Linux: Use native terminal
• Basic knowledge of Linux commands: Understanding Linux Commands .
• Pre-installed conda environments: Conda Environments.

Recommended Resources

Learn About Illumina and Oxford Nanopore Sequencing

• How Illumina Sequencing Works
• How Oxford Nanopore Sequencing Works

Linux Shell Basics

• Basic Tutorial
• Linux Basics Solutions

Linux Shell Advanced

• Advanced Tutorial
• Linux Advance Solutions

Other Linux tutorials

Linux Tutorial

Population Genetics Workshop Pipeline Breakdown

1. Initial Processing of FASTQ Files

Objective:

• Fastq File Processing

Solutions File:

• Fastq File Processing Solutions

Includes quality check (FastQC), adapter trimming (Trim Galore/trimmomatic), and preparing cleaned reads.

Check read quality (e.g., fastqc)

Trim adapters or poor-quality reads (Trim-galore, trimmomatic)

Clean FASTQ files ready for mapping

Need help understanding a FastQC report? Click the image below to watch a short walkthrough that explains key sections of the report and how to interpret them.

2. Mapping Reads to Reference Genome

Objective:

• Read Mapping And Sorting .

Solutions File:

• Read Mapping And Sorting Solutions.

Align with BWA or Bowtie2

Convert SAM to BAM, sort and index using samtools

Click the image below to watch a short walkthrough that explains BWA tool.

3. Identifying Variants (SNPs/Indels)

Objective:

Variant Identification.

Call variants using bcftools or strelka

Generate a VCF file

Optionally apply variant filtering

Click the image below to watch a detailed walkthrough that explains the variant calling process and how it fits into the genomic analysis pipeline.

4. Filtering Variants

Objective:

Variant Filtering.

Solutions File:

Variant Filtering Solution.

Explanation:

Variant Filter Descriptions.

• Apply filters with bcftools, vcftools
• Remove low-confidence variants

5. Population Structure & Visualization

Objective:

Basic Population Genetics.

Solution:

• Convert VCFs to .bed, .ped using plink
• Perform PCA to explore population structure
• Visualize and interpret clustering and outliers

Understanding PCA (Principal Component Analysis) : Click the image below to watch a clear and concise explanation of PCA — a key method for visualizing population structure and genetic variation.

Metagenomics Workshop Pipeline Breakdown

Lecture: Shades & Hues of Metagenomics – Principles, Applications, and Opportunities. Tools and Pipelines for Metagenomics.

eDNA Metabarcoding Applications

Visual overview of applications of eDNA metabarcoding in biodiversity and ecological studies.

A) Amplicon Metagenomics

Discussion

• What is a species?
• Taxonomy delimitation approaches: clustering vs denoising
• OTU: de novo, reference-based, open and closed vs ASV

Hands-on: DADA2

• Install R and R Studio
• Complete DADA2 tutorial: link
• Adapt DADA2 pipeline to dataset: link

Discussion

Diversity measurements: rarefaction, alpha vs beta diversity. Which aspects of diversity can we measure with amplicon metagenomics data?

Hands-On: Phyloseq

• Rarefaction curves
• Alpha metrics: Observed, Chao1, Shannon, Simpson
• Stacked bar charts
• Beta diversity: nMDS, PCoA, PCA

B) Shotgun Metagenomics Workflow (Microbiome Study)

1. Demultiplexing: Handled by sequencing platforms, samples identified by barcodes.
2. Quality Control: Remove low-quality reads using tools like FastQC.
3. Host DNA Removal: Filter host reads via mapping to reference genome (e.g., bwa, bowtie).
4. Taxonomy Assignment: Use tools like MetaPhlAn. Reads map to clade-specific markers to answer: “Who is in the sample?”
5. Computing Taxa Abundance: Estimate abundance from clade-specific marker mapping.
6. Visualizing Taxonomic Profiles: Use MetaPhlAn utilities (merge_metaphlan_tables, hclust2).
7. Functional Annotation: Tools like HUMAnN, eggNOG-mapper assign functions by aligning reads to ortholog groups, answering: “What do the microorganisms do?”

Metagenomics Workflow Overview

The diagram below summarizes the overall metagenomics analysis workflow — from microbiome sampling and sequencing to assembly-based profiling, taxonomic classification, functional annotation, and downstream biological interpretation.

Click the image to view the full-sized metagenomics workflow diagram.

Our Workshop Sponsors

We gratefully acknowledge the generous support of our sponsors who make this workshop possible. Their dedication to advancing genomic research and capacity building plays a vital role in wildlife conservation.