Mini-course 1 - Bacterial metagenomics
Rohit Ghai and Carolina Megumi Mizuno (EGG, UMH)
Thursday, March 27th, 08:00 - 11:00

Course outline:

  • How to make a metagenome: choosing between direct and clone sequencing
  • Sequencing: The different platforms: 454/Illumina/Ion torrent etc, pros and cons of each, choosing between paired/unpaired reads and library sizes.
  • Metagenomic analysis based on individual reads: GC plots, 16S rRNA: identification, construction of phylogenetic trees, clone library data, inclusion of metagenomic reads in reference phylogenies, search for functional domains (e.g. Pfam) in metagenomic reads and comparison of metagenomic samples based on functional domains, recruitment of reference genomes and identification of metagenomic islands.
  • Assembling the metagenome: different strategies for different technologies and library types.
  • Annotation: gene prediction, function identification (Pfam, KEGG, COG, TIGR), reconstruction of microbial genomes: using phylogenetic information and read coverage to identify related groups of contigs.
  • Ecological relevance: hints to lifestyle by identification of interesting genes/features, identification of metabolic pathways, genomic comparisons to related microbes, recruitments to access abundance.

Mini-course 2 - Phage genomics and metagenomics
Ramy Aziz (University of Cairo, State University of San Diego)
Friday,  March 28th, 08:00 - 11:00

Course outline:

  • Naming of phages
  • Sequencing technologies, coverage and centers
  • Checking sequence for errors and orientation
  • Tools for automated annotation
  • Manual curation – proofreading
  • Protein homologs and motifs
  • Consistent naming of phage proteins
  • DNA motifs – promoters & terminators
  • Submission to GenBank
  • Comparative proteomics  & genomics
  • Correct taxonomy
  • Diagrams for publications