Unicycler

Unicycler represents a solution for assembling bacterial genomes by merging the strengths of both short and long-DNA sequencing technologies. Developed to address the challenges of producing accurate and complete genome assemblies, Unicycler bridges the gap between the high accuracy but fragmented outputs typical of Illumina's short-read sequencing and the more holistic but error-prone genome assemblies produced by long-read technologies such as Pacific Biosciences and Oxford Nanopore Technologies.

At the core of Unicycler's methodology is an initial assembly graph constructed from short reads utilizing the de novo assembler SPAdes. This graph is refined and simplified with insights derived from short and long reads, showcasing Unicycler's unique ability to integrate data from these disparate sequencing technologies effectively. A novel semi-global aligner within Unicycler aligns long reads to the assembly graph, enhancing the genome assembly's structural resolution without compromising accuracy.