Capturing variation in metagenomic assembly graphs with MetaCortex.

ABSTRACT:

Motivation

The assembly of contiguous sequence from metagenomic samples presents a particular challenge, due to the presence of multiple species, often closely related, at varying levels of abundance. Capturing diversity within species, for example, viral haplotypes, or bacterial strain-level diversity, is even more challenging.

Results

We present MetaCortex, a metagenome assembler that captures intra-species diversity by searching for signatures of local variation along assembled sequences in the underlying assembly graph and outputting these sequences in sequence graph format. We show that MetaCortex produces accurate assemblies with higher genome coverage and contiguity than other popular metagenomic assemblers on mock viral communities with high levels of strain-level di

SUBMITTER: Martin S 

PROVIDER: S-EPMC9889960 | biostudies-literature | 2023 Jan

REPOSITORIES: biostudies-literature