Strainy: phasing and assembly of strain haplotypes from long-read metagenome sequencing

Bacterial species in microbial communities are often represented by mixtures of strains, distinguished by small variations in their genomes. Despite the functional importance of intra-strain heterogeneity, its characterization from metagenomic sequencing data remains challenging. Short-read approaches can be used to detect small-scale variation between strains, but fail to phase these variants into contiguous haplotypes. Long-read metagenome assemblers can generate contiguous bacterial chromosomes, but often suppress strain-level variation in favor of species-level consensus. Here we present Strainy - an algorithm for strain-level metagenome assembly and phasing from Nanopore and HiFi reads. Strainy takes a de novo metagenomic assembly as input, identifies strain variants which are then phased and assembled into contiguous haplotypes. Using simulated and mock Nanopore and HiFi metagenome data, we show that Strainy assembles accurate and complete strain haplotypes, outperforming current Nanopore-based methods and comparable with HiFi-based algorithms in completeness and accuracy. We then use Strainy to assemble strain haplotypes of a complex environmental metagenome, revealing distinct mutational patterns in bacterial species.