Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PacBio / ONT reads as input and outputs polished contigs. Flye also has a special mode for metagenome assembly. Flye is using repeat graph as a core data structure. In difference to de Bruijn graphs (which require exact k-mer matches), repeat graphs are built using approximate sequence matches, and can tolerate higher noise of SMS reads.