Strain-resolved de-novo metagenomic assembly of viral genomes and microbial 16S rRNAs

Metagenomics is a powerful approach to study environmental and human-associated microbial communities and, in particular, the role of viruses in shaping them. Viral genomes are challenging to assemble from metagenomic samples due to their genomic diversity caused by high mutation rates. In the standard de Bruijn graph assemblers, this genomic diversity leads to complex k-mer assembly graphs with a plethora of loops and bulges that are challenging to resolve into strains or haplotypes because variants more than thek-mer size apart cannot be phased. In contrast, overlap assemblers can phase variants as long as they are covered by a single read. Here, we present PenguiN, a software for strain resolved assembly of viral DNA and RNA genomes and bacterial 16S rRNA from shotgun metagenomics. Its exhaustive detection of all read overlaps in linear time combined with a Bayesian model to select strain-resolved extensions allow it to assemble severalfold more viral strain genomes and 16S rRNAs from various real and simulated short-read datasets than the state of the art.