Fig. 1

Illustration of the seed-and-bridge correction strategy using short and long k-mers. Implicit de Bruijn graphs with arbitrary k can be inferred from an FM-index. The use of a short, fixed k often does not resolve “hairball” and other structures in the graph caused by low-complexity and repetitive genomic elements. Longer K-mers may dramatically simplify the bridging step if sufficiently long seeds can be found. Illustrative seed-and-bridge paths are shown for short k-mer and long K-mer graphs. Seed k-mers are shown in orange, and the correct path in black. The two-pass (k, K) seed-and-bridge correction implemented in FMLRC allows the correction of short, nonrepetitive segments in the first pass, then seeding larger K-mers and bridging to resolve more complex sequences