Metagenomics Workshop SciLifeLab
2015-11-uppsala
  • Introduction
  • Connecting to UPPMAX
  • Checking required software
  • Quality Control
  • Community analysis using 16S reads
  • Metagenomic Assembly
  • Taxonomic Classification
  • Functional 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.

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!

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© Copyright 2014, Johannes Alneberg, John Larsson, Ino de Bruijn, Luisa Hugerth, Anders Andersson. Revision a3b49b37.

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