PEGASUS: A Comprehensive Hybrid Genome Assembly Pipeline

We introduce PEGASUS, a Pretty Epic Genome Assembly Software Using Sequences, as an all-in-one, user-friendly genome assembly tool that implements hybrid assembly methods (i.e., using both long and short read sequences) to produce reliable results. PEGASUS is written in and containerized in Nextflow to ensure reproducible results across environments. In addition to genome assembly, PEGASUS analyzes raw reads to gather statistics, and employs various methods to ensure the quality of the assembled genome allowing for a comprehensive process. PEGASUS also provides a reference genome scaffolding, which allows for high-quality genome assemblies across multiple individuals without requiring extensive read depth (if a suitable reference genome is available). This approach yields significant advantages in terms of reducing sequencing costs, assembly runtime, and computational power needed when building many genomes of the same species.