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Course Outline
Introduction to Microbial Genomics
- Overview of microbial genomics and metagenomics
- Sequencing technologies and typical study designs
- Key file formats and data organization
Quality Control and Preprocessing
- Read quality assessment and trimming
- Host removal and contamination screening
- Read normalization and downstream considerations
Taxonomic Profiling Approaches
- Marker-based profiling with MetaPhlAn
- K-mer and classification methods with Kraken2 and Bracken
- Comparing profiling outputs and visualization
Metagenome Assembly and Binning (overview)
- Assembly strategies and SPAdes usage
- Contig binning concepts and common tools (brief)
- Assessing assembly quality and completeness
Genome Annotation and MLST
- Annotating genomes with Prokka
- Performing MLST and interpreting sequence types
- Generating reports for sharing results
SNP Calling and Phylogenetics
- Mapping-based SNP calling workflows with Snippy
- Building phylogenetic trees with IQ-TREE
- Tree visualization and interpretation with iTOL
Antimicrobial Resistance and Functional Profiling
- AMR gene detection with AMRFinderPlus, CARD, and ResFinder
- Functional profiling and pathway summaries
- Reporting resistance and functional annotations
Reproducible Workflows and Best Practices
- Using Conda, Docker, and pipeline templates for reproducibility
- Data management, metadata standards, and FAIR principles
- Scaling analyses with cloud resources and notebooks
Case Studies and Hands-on Labs
- 16S/18S amplicon analysis from raw reads to taxonomic table
- Metagenomic profiling and comparative analysis across samples
- Genome assembly, annotation, SNP phylogeny, and AMR reporting
Summary and Next Steps
Requirements
- Familiarity with basic biological concepts such as DNA and genes
- Comfort with using a command-line interface is recommended
- Basic understanding of sequencing concepts and file formats (FASTQ, FASTA)
Audience
- Microbiologists
- Academic researchers
- Research staff and industry scientists interested in microbial genomics
21 Hours
Delivery Options
Private Group Training
Our identity is rooted in delivering exactly what our clients need.
- Pre-course call with your trainer
- Customisation of the learning experience to achieve your goals -
- Bespoke outlines
- Practical hands-on exercises containing data / scenarios recognisable to the learners
- Training scheduled on a date of your choice
- Delivered online, onsite/classroom or hybrid by experts sharing real world experience
Private Group Prices RRP from €6840 online delivery, based on a group of 2 delegates, €2160 per additional delegate (excludes any certification / exam costs). We recommend a maximum group size of 12 for most learning events.
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