392163 Introduction to Metagenomics and Single Cell Genomics (S) (SoSe 2014)

Over 99% of the microbial species observed in nature cannot be grown in pure culture, making it impossible to study them using classical genomic methods. Metagenomics and single cell genomics are two approaches to study the microbial dark matter.
Metagenomics studies the DNA extracted from an environmental community. Recent advances in sequencing technologies allow deep sampling of complex metagenomic communities, even with hundreds or thousands of species. Resulting data sets consist of billions of individual reads and approach terabytes in size.
A complementary approach to sequencing DNA of a whole microbial community is single cell genomics. DNA sequencing from single amplified genomes of individual cells is a novel approach in genome research, which allows to study the genomes of uncultured species from diverse environments.

After making us familiar with the specific terminology in this field, in this seminar we will address the following topics:
(1) The design, intent, and results of metagenomic and single cell studies. What are the biological questions asked? What did we learn from e.g. the human microbiome project?
(2) Challenges in data generation and analysis. Why is microbial single cell genomics that complicated (hint: sample contamination)? How can we untangle genomes from metagenomes?
(3) Algorithmic issues related to metagenomics and single cell genomics, such as assembling sequencing data with highly uneven depth or obtaining the ability to scale with data sets of tremendous size.