Metagenomics Workshop SciLifeLab
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  • Metagenomic Assembly Workshop
  • Comparative Functional Analysis Workshop
  • Comparative Taxonomic Analysis Workshop
  • Metagenomic Binning Workshop
  • Metagenomic Annotation Workshop
Metagenomics Workshop SciLifeLab
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Welcome to the Metagenomics Workshop at SciLifeLab, StockholmΒΆ

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!

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© Copyright 2014, Johannes Alneberg, Johan Bengtsson-Palme, Ino de Bruijn, Luisa Hugerth, Mikael Huss, Thomas Svensson. Revision f4b13996.

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