mosaicFlye: Resolving long mosaic repeats using long error-prone reads

Long-read technologies revolutionized genome assembly and enabled resolution of bridged repeats (i.e. repeats that are spanned by some reads) in various genomes. However the problem of resolving unbridged repeats (such as long segmental duplications in the human genome) remains largely unsolved, making it a major obstacle towards achieving the goal of complete genome assemblies. Moreover, the challenge of resolving unbridged repeats is not limited to eukaryotic genomes but also impairs assemblies of long repeats in bacterial genomes and metagenomes.

We describe the mosaicFlye algorithm for resolving complex unbridged repeats based on differences between various repeat copies and show how it improves assemblies of bacterial genomes and metagenomes.