Sylabus
1. Metagenome-Wide Association Studies Course presentation/overview and discussion about the sequencing revolution on microbial studies. Recent achievements and knowledgement increase as a result of the advances in sequencing technology.
2. Sequencing technology fundamentals Sequencing concepts, Maxam and Gilbert, Sanger, High-throughput technology (short read: 454, illumina and Ion Torrent; long read: Nanopore and PacBio) and practical library preparation.
3. Experimental design Importance of formulation of hypothesis or a research question, sampling, replication, homogenization, randomization and control.
4. Sequencing data treatment and genome assembly Quality check, phred score, expected error in high-throughput sequencing, methods for cleaning data and the problems of not working with quality filtered data and genome assembly.
5. Taxonomic profile based on amplicon data: ‘Who is there?’ Amplicon data generation introduction, ribosomal genes, phylogenetic information. Biodiversity indices, microbial ecology concepts and metataxonomic data visualization.
6. Genomics, Metagenomics and Shotgun data handling Gene prediction, functional annotation, taxonomy assignment, binning strategies, genomes assembled from metagenomes and data visualization.
7. Analysis of RNA and Metatranscriptomics Concepts, methods, applications, sampling and RNA preservation techniques.
8. Technical demonstration of the most used methods for high-throughput sequencing data manipulation High-throughput sequencing data treatment (fastqc, trimmomatic and vsearch), genome assembly (spades and velvet), amplicon and metagenomic data handling, taxonomy and functional assignment (the Seed, QIIME, KEGG and BLAST).
Anotace
Kurs představí hlavní metody masivně paralelního sekvenování používané při studiu mikrobiomu. Studenti se seznámí s metodami pro hodnocení zastoupení různých druhů ve společenstvu pomocí sekvencování genomu, metagenomiky a metatranskriptomiky.
Důležitou součástí kursu je plánování projektu, navržení experimentu, zpracování dat a prezentace výsledků.