Capturing variation in metagenomic assembly graphs with MetaCortex

MotivationThe 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. ResultsWe 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 diversity, and on simulated communities containing simulated strains. Availability and ImplementationSource code is freely available to download from https://github.com/SR-Martin/metacortex, is implemented in C and supported on MacOS and Linux. Contactrichard.leggett@earlham.ac.uk Supplementary informationSupplementary materials are available at the journals website. All assemblies, simulated reads, and simulated genomes used in this paper have been deposited online on Zenodo and can be found at DOI 10.5281/zenodo.6616437.