In this training course you will find theory and practice material for introducing yourself to wgs analysis for foodborne bacteria. Here you will find the agenda.
The material includes slides with theory concepts and a practical exercises using Galaxy trainings, focusing on the interpretation of results.
- Talk 1: Massive sequencing of bacterial genomes. State-of-the-art. & Bacterial genomes sequencing. Applications.
- Talk 2: Incorporation of massive sequencing in the laboratory. Massive sequencing technologies. Sequencing by synthesis in Illumina. The MiSeq sequencer. Kits and specifications.
- Talk 3: Extraction and characterization of nucleic acids. Use of SPRI for the purification, concentration and selection of DNA. Library preparation for Illumina sequencing. Illumina Library Prep Kits: PCR and PCR free. Preparation kits from other suppliers and robotization. 16S Metagenomics, Library Preparation, and MiSeq Analysis Indexing. Single and double indices and combinatorial and unique indices
- Talk 4: Quantification and pooling of libraries. Saturation normalization, qPCR and analytical sequencing. Preparation of sample sheets. IEM. Commissioning the MiSeq instrument. Quality parameters in sequencing. Charge density, Q30 and passing filters. BaseSpace
- Talk 5: Analysis of genomic data in bacteriology, options and methodologies
- Talk 6: Organization, storage and management of genomic data
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Talk 7: Genomic data quality analysis
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Talk 8: Genome assembly
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Talk 9: Genome Annotation
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Exercise 1: Introduction to Galaxy - Download PDF file
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Talk 10: Alignment against reference genome and calling variants: identification of SNPs.
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Talk 12: Gene-by-gene approach vs SNPs
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Exercise 2: Quality control in Galaxy
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Talk 13: Course summary. Study of an outbreak, design, sequencing and analysis
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Exercise 3: Genome assembly and annotation of prokaryotic in Galaxy
Course queue: https://usegalaxy.eu/join-training/virologist_isciii