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DTSTART;TZID=Africa/Nairobi:20250722T080000
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SUMMARY:3rd Hands-On Wildlife Genomics Workshop
DESCRIPTION:Welcome to Wildlife Genomics 3 workshop\nDive into the Wild World of Genomics and Metagenomics!\nJoin 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. \nOn 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! \nAlternatively\, 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. \nWhether 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. \n \n\nGeneral Information\n\nDate: July 22- 04 August\, 2025\nLocation: Pwani University\, Kilifi\, Kenya\nOrganized by: Pwani University and Indian Institute of Science (IISc)\nPrice: Free\nContact: s.wambua@pu.ac.ke\, anubhabkhan@gmail.com\n\n\nWorkshop Objectives\n🧬 Population Genomics Track\n\nUnderstand and process raw sequencing data (FASTQ format)\nPerform quality control and preprocessing\nMap reads to a reference genome\nIdentify variants (SNPs and indels)\nUse filtered variants for basic population genetic analysis (PCA\, Admixture\, heterozygosity)\n\n🧪 Metagenomics & eDNA Track\n\nIntroduce participants to eDNA metabarcoding and shotgun metagenomics workflows\nProvide hands-on experience in field collection\, DNA extraction\, and library preparation\nTrain participants in sequence quality control\, taxonomic assignment\, and diversity metrics\nExplore use cases in wildlife health\, habitat quality assessment\, and ecosystem monitoring\n\nTake a look at our reproducible version of other workshops\, available at: PoODL-CES Workshops \n\nPreliminary Workshop Schedule\n\n\n\nDay\nPopulation Genomics Track\nMetagenomics Track\n\n\n\n\nDay 01\nWelcome and orientation. Theory: Basics of genomics – Principles\, Applications\, and Opportunities. Sampling Techniques and Their Impact on Results. Planning sampling strategies.\n\n\nDay 02\nFieldwork: Collection of environmental samples. Laboratory session: DNA extraction. Theory: Troubleshooting common issues in DNA extraction.\n\n\nDay 03\nPractical: Library preparation\, DNA quantification and quality control\, Sequencing. Theory: Sequencing Platforms\, Overview of sequencing outputs and formats (e.g.\, FASTQ)\, applications of sequence data\, sequencing strategies\, Basic Linux and command line\n\n\nDay 04\nTheory: Introduction to population genetics\, conservation genetics\, evolution and genomics\nTheory: Basics of Metagenomics – Principles\, Applications\, and Opportunities.Tools and Pipelines for Metagenomics\n\n\nDay 05\nHow to design your wildlife genomics project\, Basic linux2\, Accessing freely available data for research.\nPractical: Setting up a bioinformatics environment (local or cloud-based). Theory: Introduction to raw data quality assessment (e.g.\, FastQC).\n\n\nDay 06\nMapping\, SNP calling\, SNP filtering (step 1).\nTheory: Quality Control and Filtering of Sequencing Data\, Introduction to taxonomic classification using databases (e.g.\, SILVA\, RDP)\, Practical: Trimming and filtering data\, Assigning taxonomy to sequences.\n\n\nDay 07\nSNP filtering step2\, Relatedness\, PCA(Principal Component Analysis)and Admixture.\nTheory: Functional Annotation and Pathway Analysis. Practical: Annotation using tools like Prokka or EggNOG-mapper\, Visualizing functional data.\n\n\nDay 08\nMeasuring genetic diversity: Heterozygosity\, Pairwise Nucleotide Diversity (pi) Allelic richness and Inbreeding.\nTheory: Diversity Analysis – Alpha and Beta Diversity Metrics\, Introduction to statistical tools for metagenomics (e.g.\, R\, STAMP). Practical: Diversity calculations and visualizations\, Statistical comparisons between samples.\n\n\nDay 09\nDemographic history\, why is it important? How to estimate it? PSMC\, GONE.\nWorkshop: Interpreting taxonomic and functional analysis results. Case studies: Examples of published metagenomic studies. Group activity: Preparing a presentation on findings. Individual feedback and troubleshooting session.\n\n\nDay 10\nSelection/load. How to measure it? Identifying deleterious alleles and signatures of selection.\nGroup presentations of results. Peer and instructor feedback. Discussion: Ethical considerations in metagenomics.\n\n\n\n\n\nInstructors\n \nPre-requisites & Setup\n\nAccess to a Unix/Linux shell environment:\n\nWindows: Install MobaXterm\nMac/Linux: Use native terminal\n\n\nBasic knowledge of Linux commands: Understanding Linux Commands .\nPre-installed conda environments: Conda Environments.\n\nRecommended Resources\nLearn About Illumina and Oxford Nanopore Sequencing\n\nHow Illumina Sequencing Works\nHow Oxford Nanopore Sequencing Works\n\nLinux Shell Basics\n\nBasic Tutorial\nLinux Basics Solutions\n\nLinux Shell Advanced\n\nAdvanced Tutorial\nLinux Advance Solutions\n\nOther Linux tutorials\n\nLinux Tutorial\n\nPopulation Genetics Workshop Pipeline Breakdown\n1. Initial Processing of FASTQ Files\nObjective: \n\n\n\nFastq File Processing\n\n\n\nSolutions File: \n\nFastq File Processing Solutions\n\nIncludes quality check (FastQC)\, adapter trimming (Trim Galore/trimmomatic)\, and preparing cleaned reads. \n\nCheck read quality (e.g.\, fastqc)\nTrim adapters or poor-quality reads (Trim-galore\, trimmomatic)\nClean FASTQ files ready for mapping\n\nNeed 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. \n\n2. Mapping Reads to Reference Genome\nObjective: \n\n\n\nRead Mapping And Sorting .\n\n\n\nSolutions File: \n\nRead Mapping And Sorting Solutions.\n\n  \n\nAlign with BWA or Bowtie2\nConvert SAM to BAM\, sort and index using samtools\n\nClick the image below to watch a short walkthrough that explains BWA tool. \n\n3. Identifying Variants (SNPs/Indels)\nObjective: \n\nVariant Identification.\n\n  \n\nCall variants using bcftools or strelka\nGenerate a VCF file\nOptionally apply variant filtering\n\nClick the image below to watch a detailed walkthrough that explains the variant calling process and how it fits into the genomic analysis pipeline. \n\n4. Filtering Variants\nObjective: \n\nVariant Filtering.\n\nSolutions File: \n\nVariant Filtering Solution.\n\nExplanation: \n\nVariant Filter Descriptions.\nApply filters with bcftools\, vcftools\nRemove low-confidence variants\n\n5. Population Structure & Visualization\nObjective: \n\nBasic Population Genetics.\n\nSolution: \n\n\n\nConvert VCFs to .bed\, .ped using plink\nPerform PCA to explore population structure\nVisualize and interpret clustering and outliers\n\n\n\nUnderstanding 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. \n\n\nOur Workshop Sponsors\nWe 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.
URL:https://www.recourse.co.ke/event/3rd-hands-on-wildlife-genomics-workshop/
LOCATION:Pwani University\, Kilifi\, Kenya\, Pwani University\, Kilifi\, 80108\, Kenya
ORGANIZER;CN="Indian Institute of Science":MAILTO:sccs@sccs-bng.org
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