Abstract

Computer scientists have repeatedly proven that genome assembly, even for a single organism, is an intractable computational problem. In metagenomics, the problem is even harder – we are trying to simultaneously reconstruct many different and not so different genomes. Should we even try?

In my talk I will outline the main reasons to be pessimistic about metagenomic assembly and discuss possible ways forward. In particular, I will argue that ‘metagenomic assembly’ is an ill defined concept and that we, as a community, need to identify and formalize specific use cases that address relevant biological problems and that are computationally tractable. I will also discuss issues related to the validation of metagenomic assemblies, an important yet often overlooked problem.