Summer school in Bioinformatics 2025
This year the summer school will be
held from 1-5th September at the Biotechnical faculty of the
University of Ljubljana in Ljubljana, Slovenia
Bioinformatic Summer School: Comparative Genomics, Nanopore Metagenomics and Metataxonomic Analysis
The overall teaching aim of this module is to create competence in the students allowing them to independently perform bioinformatic analysis using the command line. This includes comparative analysis on bacterial (meta)-genomes and metataxonomic analysis.
The overall teaching aims of the summer school is to create competence in the students in terms of independently performing bioinformatic analysis on the command line. This includes comparative analysis on bacterial (meta)-genomes and metataxonomic analysis. A student will learn through examples from practice, how to analyse genetic content within bacterial organisms and engage in discussions regarding the biological implications stemming from phylogenetic relationships, genetic content, microbial composition, and their interrelationships. The programme of summer school represents the combination of knowledge from the fields of informatics and biology and focuses on individual practical work in an international group of students. The target participants are students of Microbiology, Biotechnology, Biology, Genetics (BSc, MSc, PhD students).
Students will gain proficiency in utilizing the Linux command line, demonstrate competence in utilizing recommended command line tools and be able to conduct literature reviews in bioinformatics to identify additional tools pertinent to addressing biological inquiries. They will also be able to determine the composition of microbiomes through analytical techniques and analyse genetic content within bacterial organisms to deduce biological significance. They will engage in discussions regarding the biological implications stemming from phylogenetic relationships, genetic content, microbial composition, and their interrelationships.
Over the course of the summer school, participants will delve into the intricate world of genomic assembly, annotation, and metagenomic analysis. In general, the assembly of genomes using short reads (SPAdes), long reads (Flye), and hybrid approaches (Unicycler), followed by genome annotation using Bakta will be addressed. Functional profiling of genomes will be covered, focusing on secondary metabolites prediction (antiSMASH) and carbohydrate-active enzymes (CAZYmes) annotation with dbCAN. Next, participants will venture into long-read metagenomics, learning to assemble small metagenomes with metaFlye and taxonomically classify metagenomic contents using 16S rRNA amplicon sequencing (barrnap) and kmer-based methods (Kraken2). The week will conclude with insights into taxonomic analysis of microbiomes, including 16S rRNA amplicon sequencing data classification (DADA2), visualization, and statistical analysis of microbiome data using vegan.
For comparative genomics we will:
- Download all genomes of a bacterial species.
- Annotate the genetic content of these genomes
- Profile the prophage content of these genomes
- Profile the secondary metabolism of these genomes
- Build a whole-genome phylogeny of the genomes
- Infer the linkage between data-driven analysis and fundamental biology
For metagenomics we will:
- Download metagenomic data
- Filter long read nanopore sequences
- Assemble nanopore sequences into metagenomes
- Analyze metagenomic sequences using methods from comparative genomics
For metataxonomy we will :
- Download 16S data
- Demultiplex the data
- Clean, filter and denoise the data
- Taxonomically classify the data
The successful student will
- Have a working knowledge of the Linux command line
- Be able to use suggested command line tools
- Investigate the bioinformatic literature to find further tools relevant for the biological questions
- Infer the biological relevance of the genetic content in bacteria
- Infer the composition of microbiomes
- Discuss the biological implications of phylogeny, genetic content, microbial composition and the relatedness of all the above