CulebrONT: a streamlined long reads multi-assembler pipeline for prokaryotic and eukaryotic genomes

Abstract

Using long reads provides higher contiguity and better genome assemblies. However, producing such high quality sequences from raw reads requires to chain a growing set of tools, and determining the best workflow is a complex task. To tackle this challenge, we developed CulebrONT, an open-source, scalable, modular and traceable Snakemake pipeline for assembling long reads data. CulebrONT enables to perform tests on multiple samples and multiple long reads assemblers in parallel, and can optionally perform, downstream circularization and polishing. It further provides a range of assembly quality metrics summarized in a final user-friendly report. CulebrONT alleviates the difficulties of assembly pipelines development, and allow users to identify the best assembly options.