Genome-resolved metagenomics internal workshop
Antton will be organising a whole-day workshop about genome-resolved metagenomics on the 8th of September, Friday. It will be an intensive session introducing key concepts, procedures and resources for reconstructing and annotation prokaryotic genomes from metagenomic mixtures, quantifying their presence in metagenomic samples, estimating multiple diversity metrics (including phylogenetic and functional features), result visualisation and statistical modelling.
NB! the workshop is already full with the maximum of 20 attendees already signed up. However, as many people who cannot attend the workshop the next week have expressed their interest in participating, Antton will organise a second workshop probably in November.
AGENDA (tentative)
Microbiomes and their characterisation (08.30 - 09:15): introduction and key biological and technical concepts
Sample collection, preservation and laboratory processing (09.15 - 10:00): how to generate high-quality data
Morning break
Bioinformatic pre-processing (10.30 - 11:00): most relevant procedures of the initial bioinformatic steps
Metagenomic assembly and binning (11.00 - 12:00): tools and strategies for efficient assembly and binning, as well as taxonomic and functional annotation
Lunch break
Microbial community quantitation (13:00 - 13:45): strategies to quantify presence of prokaryotes accounting for known biases
Microbiome diversity assessment (13:45 - 14:30): using Hill numbers for alpha and beta diversity estimation, including neutral phylogenetic and functional components
Afternoon break
Microbiome variation assessment (15:00 - 15:45): ordination and dimensionality reduction, and univariate and multivariate analyses to study microbial communities
Conclusions and assessment (15:45 - 16:00)