Metagenomics Workshop SciLifeLab
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  • Introduction
  • Connecting to UPPMAX
  • Checking required software
  • Quality Control
  • Community analysis using 16S reads
  • Metagenomic Assembly
  • Annotation
Metagenomics Workshop SciLifeLab
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  • Welcome to the Metagenomics Workshop in Uppsala
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Welcome to the Metagenomics Workshop in UppsalaΒΆ

This is a one day metagenomics workshop. We will discuss quality checking, assembly, taxonomic classification, binning and annotation of metagenomic samples. The workshop is developed by the Environmental Genomics group at KTH / SciLifeLab.

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
    • 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
  • Annotation
    • Functional Annotation
    • Taxonomic annotation
    • Mapping reads and quantifying genes
    • Summarize and explore the annotation

Enjoy!

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© Copyright 2014, Johannes Alneberg, John Sundh, Ino de Bruijn, Luisa Hugerth, Anders Andersson. Revision ac59a5ee.

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