Analysing Whole-Genome Shotgun Metagenomic Data

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   IMPORTANT DATES for this Course
   Deadline for applications: June 21st 2013
   Notification of acceptance within 72 hours of application.
   Course date: June 27th and June 28th 2013


Nick Loman worked as a medical doctor before studying for a PhD in genomics with Prof Mark Pallen at the University of Birmingham. His research interest is the application of high-throughput sequencing to the study of bacterial pathogens, particularly those causing outbreaks in hospitals and in the community including Acinetobacter baumannii, Pseudomonas aeruginosa, Mycobacterium tuberculosis, Escherichia coli and Streptococcus pneumoniae (see these references). Nick is enthusiastic about the use of Internet communication in Science and Medicine, and was instrumental in kick-starting the crowd-sourcing analysis of the German E. coli outbreak strain in June 2011, as published in Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4. He writes a popular blog on genomics and sequencing - Pathogens: Genes and Genomes - as well as maintaining a Twitter feed (@pathogenomenick). Nick has 5 years experience of high-throughput sequencing technologies and their associated analytical pipelines.

Affiliation: Independent Research Fellow, Institute of Microbiology and Infection, University of Birmingham, Birmingham ,UK

Chris Quince is an expert in the analysis of next generation sequence data from microbial communities. He leads a group based at the University of Glasgow developing novel algorithms and statistics for interpreting both 16S amplicon and metagenome data. These include applications for noise-removal from 454 pyrosequenced amplicons and novel statistics for diversity estimation and community clustering. They apply these methods to communities spanning a range of environments from the human microbiome to soils and engineering systems.

Affiliation: University of Glasgow, Glasgow, UK

Anders Andersson received his PhD in 2005 at the KTH Royal Institute of Technology, Department of Biotechnology after graduate studies on functional genomics. Thereafter he conducted postdoctoral studies at the Karolinska Institute, University of California Berkeley, and at Uppsala University, working with metagenomic analysis of various ecosystems. Since 2010 Andersson is an assistant professor at the Science for Life Laboratory/KTH in Stockholm where his group works with NGS-based metagenomics and 16S/18S amplicon sequencing. The major focus is the Baltic Sea, where the work follows two major trajectories: I) to model the microbial ecological network that underpins the pronounced season dynamics in microbial community composition of surface waters, II) to reconstruct the genomes of the main microbial players. He is also involved in projects exploring other microbiomes, such as the human gut microbiota. To enable these projects his group develops molecular as well as bioinformatics methods for community analysis.

Affiliation: KTH / SciLifeLab, Stockholm, Sweden

Josh Quick is a bioinformatician at the University of Birmingham, working on Pseudomonas infections in the hospital environment through whole-genome shotgun sequencing and metagenomics. Prior to working in Birmingham he was a systems integrator for Illumina responsible for the development of the MiSeq sequencing platform.

Affiliation: Institute of Microbiology and Infection, University of Birmingham, UK

Course description

In this two-day intermediate-level course we will cover the basics of analysing whole-genome shotgun metagenomics data generated from high-throughput sequencing instruments. This would interest those interested in taxonomic and functional characterisation of complex microbial communities from clinical or environmental samples. Topics covered will include design of sequencing experiments, quality control of data, de novo assembly and co-assembly, mapping reads to reference assemblies, contig clustering, whole-genome and haplotype reconstruction methods, taxonomic assignment of contigs, and cross-sample comparisons of microbial communities.

Target Audience

The course will suit those already familiar with bioinformatic analysis of microbial whole-genome sequences and/or 16S phylogenetic profiling who now wish to gain knowledge of new techniques for whole-genome metagenomic studies.

Course Pre-requisites

The course will be performed on Linux workstations and will feature a large hands-on component with real datasets, therefore knowledge of the UNIX command-line is essential, as well as familiarity with microbial genomics and ecology and a basic grasp of statistics.

Detailed Program

Instituto Gulbenkian de Ciência,

Apartado 14, 2781-901 Oeiras, Portugal

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Last updated:  May 20th 2013