Grouping reads and labeling recombinants. A "strained" scaffold shown at different zoom levels: (A) full scaffold, (B) a few thousand bases, (C) viewing individual SNPs. Environmental reads were aligned to scaffold 29 from Ferroplasma type II and manually grouped into strains. Reads placed in different strains from their mate-pairs are marked with red outlines and are linked to their mate-pairs by diagonal red lines. Also marked in red are read pairs which are placed in the same strain, but at least one read had a small region that matched a different strain.