Alexander Sczyrba, Sebastian Jünemann, Sebastian Jaenicke, Madis Rumming, Irena Maus (BiGi)
23.11.2015 – 25.11.2015
This course will broach the issues of targeted (16S rDNA operon gene amplicons) and untargeted (whole-genome shotgun; WGS) metagenome analysis based on high throughput next-generation sequencing (NGS) data. The first part will cover different aspects of general NGS data handling and present different techniques and tools for quality measurement, filtering, and sequence correction. On demand, a compact introduction into the Linux operating system and the usage of the command line interface will be given to guarantee a consistent baseline for the following days. The second part of this course focuses on 16S amplicon data analysis utilizing the favorite command line tool QIIME and mothur. The main aspects here are the common pipeline steps beginning with pre-processing, OTU clustering, taxonomic classification, normalization, and different statistical measurements like rarefaction analysis. Problems and pitfalls as well as the correct usage of different specialized data bases will be discussed with the attendants in conclusion. In the third part, advantages and disadvantages of whole metagenome sequencing will be illustrated. As WGS metagenomics has the potential to address the full spectra of genome-based issues, the focus here will be on taxonomic and functional analysis with the aid of different bioinformatic tools.Two different techniques to analyze WGS metagenome data are part of this section: (1) in the read-based approach the software solution MGX, an integrated platform for metagenome analysis and data visualization, will be demonstarted. (2) the assembly-based approach reconstructs genomes by assembling reads into contigs which are subject to binning methods to group individual contigs into genome bins. For analyzing metagenomics assemblies the EMGB platform will be demonstrated.
Qiime, MGX, MetaBat, MegaHit
Dr. Alexander Sczyrba
For more information see http://www.cebitec.uni-bielefeld.de/polyomics/index.php/training