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

ABSTRACT:

Background

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 the k-mer size apart cannot be phased. In contrast, overlap assemblers can phase variants as long as they are covered by a single read.

Results

Here, we present PenguiN, a software for strain resolved assembly of viral DNA and RNA genomes and bacterial 16S r

SUBMITTER: Jochheim A 

PROVIDER: S-EPMC11443906 | biostudies-literature | 2024 Oct

REPOSITORIES: biostudies-literature