JAZZ: A Whole Genome Shotgun Assembler

We present JAZZ, a new graphical algorithm for whole genome assembly that self-consistently treats paired-end constraints. JAZZ is designed to be scalable for application to large animal and plant genome sequencing projects. To aid in the development and validation of assemblies, we have also developed a suite of graphical tools for examining and manipulating large assemblies. JAZZ has been used at the JGI to assemble the genomes of many microbes, a basidiomycete fungus, and two chordates, the sea squirt Ciona intestinalis and the Japanese pufferfish Fugu rubripes; long, extremely accurate scaffolds are recovered that are excellent substrates for annotation. We discuss the challenges faced in assembling these genomes, and strategies for future sequencing projects.