Welcome to the Metagenomics Workshop in Uppsala

This is a one day metagenomics workshop. We will discuss quality checking, assembly, taxonomic classification, binning and annotation of metagenomic samples.

Here is a link to the official homepage for the SciLifeLab workshop in metagenomics.

A presentation for this workshop is available here.

Program:

• Getting started

  • Introduction
  • Connecting to UPPMAX
  • Checking required software

• Sessions

  • Quality Control
  • Community analysis using 16S reads
  • Metagenomic Assembly
  • Taxonomic Classification
  • Functional Annotation

Contents:

• Introduction
• Connecting to UPPMAX
  • Connecting to UPPMAX
  • Getting a node of your own
  • Load virtual environment
  • Set sample variables
• Checking required software
  • Programs used in this workshop
  • Using which to locate a program
  • Check all programs in one go with which
  • (Optional excercise) Install sickle by yourself
• Quality Control
  • Quality Control with FastQC
  • Optional: Quality trimming Illumina paired-end reads
• Community analysis using 16S reads
  • Community analysis using rRNA gene reads
• Metagenomic Assembly
  • Assembling reads with Velvet
• Taxonomic Classification
  • Phylogenetic Classification using Phylosift
• Functional Annotation
  • Annotating the assembly using the PROKKA pipeline
  • Predicting metabolic pathways using MinPath
  • Mapping reads and quantifying genes
  • Summarize and explore the functional annotation

Enjoy!