Welcome to the Metagenomics Workshop at SciLifeLab, Stockholm

This is a three day metagenomics workshop. We will discuss assembly, binning and annotation of metagenomic samples.

Program:

• Day 1 Time 14-17

  • Metagenomic Assembly Workshop
  • Comparative Functional Analysis Workshop
  • Comparative Taxonomic Analysis Workshop

• Day 2 Time 14-17

  • Metagenomic Binning Workshop

• Day 3 Time 13.30-17

  • Metagenomic Annotation Workshop

Contents:

• Metagenomic Assembly Workshop
  • Checking required software
  • Quality trimming Illumina paired-end reads
  • Assembling reads with Velvet
  • Mapping reads back to the assembly
• Comparative Functional Analysis Workshop
  • Gene finding
  • Functional annotation
  • Determine gene coverage in metagenomic samples
  • Comparative functional analysis with R
• Comparative Taxonomic Analysis Workshop
  • Extracting rRNA encoding reads and annotating them
  • Visualising taxonomy with KRONA
  • Comparative taxonomic analysis with R
• Metagenomic Binning Workshop
  • Setup Environment
  • CONCOCT - Clustering cONtigs with COverage and ComposiTion
  • Phylogenetic Classification using Phylosift
• Metagenomic Annotation Workshop
  • Checking required software
  • Translating nucleotide sequences into amino acid sequences
  • Search amino acid sequences with HMMER against the Pfam database
  • Normalization of count data from the metagenomic data sets
  • Estimating differentially abundant protein families in the metagenomes
  • Bonus exercise: Using Metaxa2 to investigate the taxonomic content

Enjoy!