Strainberry: automated strain separation in low-complexity metagenomes using long reads.

ABSTRACT: High-throughput short-read metagenomics has enabled large-scale species-level analysis and functional characterization of microbial communities. Microbiomes often contain multiple strains of the same species, and different strains have been shown to have important differences in their functional roles. Recent advances on long-read based methods enabled accurate assembly of bacterial genomes from complex microbiomes and an as-yet-unrealized opportunity to resolve strains. Here we present Strainberry, a metagenome assembly pipeline that performs strain separation in single-sample low-complexity metagenomes and that relies uniquely on long-read data. We benchmarked Strainberry on mock communities for which it produces strain-resolved assemblies with near-complete reference coverage and 99.9%

SUBMITTER: Vicedomini R 

PROVIDER: S-EPMC8302730 | biostudies-literature | 2021 Jul

REPOSITORIES: biostudies-literature