Metagenomics Analysis with MEGAN6

Learn how to use the most powerful interactive microbiome analysis tool

In a nutshell

  • Learn the fundamentals of NGS
  • Understand read alignment to a reference database
  • Preprocess alignment files for MEGAN6
  • Explore results in MEGAN6
  • Write small scripts for batch analyses

17 - 19 October 2017

Frankfurt, Germany

This introductory workshop provides an intensive training in how to use MEGAN6.

MEGAN6 is a comprehensive toolbox for interactively analyzing microbiome data. It comprises all the interactive tools you need for your metagenomics analysis.

  • Taxonomic analysis using the NCBI taxonomy or a customized taxonomy such as SILVA
  • Functional analysis using InterPro2GO, SEED, eggNOG or KEGG
  • Bar charts, word clouds, Voronoi tree maps and many other charts
  • PCoA, clustering and networks
  • Supports metadata
  • MEGAN6 parses many different types of input

All participants will learn how to use both the Community and Ultimate Editions of MEGAN6. For the latter, everyone will get a free 30 day license key.

Check our course layout.


The Community Edition of MEGAN6 is free to use for everyone.

MEGAN6 Ultimate Edition brings a command-line mode for automating batch analyses, advanced viewer for exploring long-read annotations, and integration of official KEGG metabolic pathways (which are no longer free, even for academic use). MEGAN6 Ultimate Edition is $2,990.00 per year per user.

This workshop has been adapted to the needs of beginners and comprises this three course modules:

  1. Aligning reads to reference database:
    The input for MEGAN is a set of sequence alignments between the sample sequences and a suitable reference database. This module will demonstrate the use of DIAMOND, which was developed in coordination with MEGAN.
  2. Meganizing alignment files:
    This module covers available procedures for importing alignments from one or more SAM, BLAST, or DIAMOND Alignment Archive (DAA) files.
  3. Exploring results in MEGAN:
    Once the alignment results have been “meganized” to annotate each query sequence by taxonomy and metabolic function, the annotations can be interactively explored in MEGAN.
  4. Scripting for batch analyses:
    This module demonstrates how to automate certain common tasks for batch analysis of files from large or recurring projects.
  5. Long-read analysis:
    Illumina short-reads remain the most popular for metagenomic studies, but interest in the use of long-reads has grown alongside the increasing popularity of PacBio and Oxford Nanopore sequencing technologies. This module covers the differences between short- and long-read analysis with MEGAN.

Detailed Course Program

Aligning reads to reference database

  • Introduction to NGS
  • Raw sequence files (FASTQ format)
  • Preprocessing of raw reads: quality control (FastQC), adapter clipping, quality trimming
  • Introduction to read mapping (Alignment methods, Mapping heuristics)
  • Read mapping (BLAST, LAST, DIAMOND)
  • Mapping output (BLAST, DAA format)

Meganizing alignment files

  • Importing alignment files using the graphical wizard
  • Taxonomic annotation (NCBI nr)
  • Metabolic annotation (INTERPRO, GO, PFAM, SEED, and KEGG)
  • Understanding MEGAN’s LCA algorithm
  • Updating annotations using different LCA parameters

Exploring results in MEGAN

  • Overview of the main taxonomy tree viewer
  • Rarefaction analysis
  • Visualizing trends and correlations
  • Comparing multiple samples
  • Handling meta-data
  • Overview of metabolic annotation visualization options
  • Importing and viewing annotations generated from another tool

Scripting for batch analyses

  • Meganizing many alignment files from the command-line
  • Introduction to scripting in MEGAN
  • Selected advanced scripting examples

Long-read analysis

  • Long-read mapping (LAST)
  • Meganizing long-reads
  • Overview of the MEGAN long-read viewer


Dr. Ted Gibbons (Computomics GmbH)
Ted worked on the Human Microbiome Project and specializes in metagenomics analysis in his current position as a Bioinformatics Scientist at Computomics.

Dr. Mario Fasold (ecSeq Bioinformatics GmbH)
Mario works in the analysis of microarray data since 2007 and developed several bioinformatics tools such as the Bioconductor package AffyRNADegradation and the Larpack program package. Since 2011 he specialized in the field of NGS data analysis and helped analysing sequencing data of several large consortium projects. Publications


  • basic understanding of molecular biology (DNA, RNA, gene expression, PCR, ...)

The target audience is biologists or data analysts with no or little experience in metagenomics.

  •   Course materials
  •   Catering during the workshop
  •   Conference dinner
  •   High-performance workstations (no laptop needed)


Location: Com Center Frankfurt, Dreieichstraße 59, Frankfurt
Language: English
Available seats: 30 (first-come, first-served)

Registration Fee: 989 EUR (excluding VAT)

Travel expenses and accommodation are not covered by the registration fee.

Travel Information - Frankfurt

Key dates

Opening Date of Registration: 1 May 2017
Closing Date of Registration: 1 October 2017
Workshop: 17 - 19 October 2017 (9 am - 5 pm)

When you register for this workshop you are agreeing with our Workshop Terms and Conditions. Please read them before you register.

Any Questions? Please feel free to contact our events team.

ecSeq Bioinformatics GmbH
Sternwartenstr. 29
D-04103 Leipzig