Episode notes
One of the ambitious goals of whole-metagenome sequencing (WMGS) is to obtain full genome assemblies of hundreds or thousands of novel unculturable microbes. It is challenging because the sequencing data contain DNA from hundreds or thousands of organisms with vastly different abundances. Highly abundant organisms generate large numbers of reads and can dominate the dataset, while low-abundance organisms may have insufficient coverage for reliable assembly. In addition, closely related organisms can contribute highly similar sequences, making it difficult to assign reads and assembled contigs to the correct organism.
These challenges have led to the development of a variety of metagenome assembly strategies, broadly including alignment-based (reference-guided) and composition-based (de novo) approaches. The choice of strategy depends on the availability of reference genomes, the complexity of the microbial community, and the abundance and divergence of the organisms present.