Microbiome science explores microbial communities in the context of health, the environment and biotechnology. Reads are collected using both short- and long-read sequencing technologies, optionally assembled, and then subjected to taxonomic and functional analysis. A detailed analysis can be obtained by first aligning all sequences against the NCBI-nr protein database using DIAMOND and then performing taxonomic and functional binning using MEGAN.

 

This workshop aims at giving an introduction to the computational analysis of microbiome sequencing reads. We briefly first discuss quality control, processing and sequence assembly. We will then discuss in more detail how to perform DIAMOND alignment of the data and how to process the resulting alignment files so as to be able to open them in MEGAN. We will then  use MEGAN to explore a number of different microbiome datasets from different host-associated studies, and from bio-reactor communities. We will consider both short-read and long-read datasets. DIAMOND is a command line tool that is run on a server. MEGAN is an interactive microbiome exploration tool that is run on a laptop or desktop.

 

The DIAMOND+MEGAN pipeline is the archetype of homology-based microbiome analysis and so obtaining an understanding of this approach will also prepare you to work with other microbiome analysis tools that follow this approach.

Who is this course for?

All people interested in gaining experience on metagenome analysis using MEGAN.