Flye

Flye is a long-read de novo assembler that can assemble bacterial genomes using only long reads from sequencing technologies like Oxford Nanopore Technologies (ONT) or Pacific Biosciences (PacBio). After assembling the genome with Flye using long reads, the assembly can be polished using short reads from Illumina sequencing with a tool like Pilon to improve accuracy.

However, the study found that a hybrid assembly approach using the assembler Unicycler, which combines both long reads (ONT or PacBio) and short reads (Illumina) in the assembly process, resulted in more accurate and complete bacterial genome reconstructions compared to the long-read-only assembly with Flye followed by polishing with Pilon. The hybrid approach was particularly effective for resolving complex, repetitive genetic structures often found in bacteria from the family Enterobacteriaceae.