Fig. 1. Strainberry pipeline.

The pipeline starts from a strain-oblivious assembly and the corresponding set of reads. It then performs haplotype phasing on the strain-oblivious assembly to separate reads into groups that likely correspond to strains. Each group is assembled separately. A final scaffolding step is used to connect sequences likely corresponding to the same strain. The pipeline performs $n-1$ iterations, where $n$ is the maximal number of detected conspecific strains.