Fig. 4

Strain-resolved metagenome assembly. a Given a pooled sequencing sample, the goal of strain-resolved metagenome assembly is to reconstruct all individual microbial strains. b A typical workflow consists of four steps: de novo assembly, contig binning, bin-wise re-assembly, and assembly curation. Each step can be performed at the species-level or at the strain-level, as illustrated in the left and middle column, respectively. Some workflows skip the initial de novo assembly step and perform strain-resolved binning directly on the sequencing reads, which can be reference-guided (right column)