HiFi-Helper: A reproducible workflow for genome assembly from HiFi reads alone

Abstract

The PacBio Revio simplifies genome assembly by generating very long reads with very few errors at an affordable price point. Comparative ease of assembly is democratizing access, leading to a larger niche for assembly workflows. HiFi-Helper is a user-friendly snakemake workflow designed to facilitate genome assembly from HiFi data alone. This tool produces a visual summary that provides intuitive feedback on the quality of the resulting assembly and guides assembly parameter optimization. The case studies presented here confirm that HiFi-only assemblies produced by HiFi-helper can meet or exceed the quality of genomes assembled in prior decades with a much lower investment of time and resources.