Snakemake workflows for long-read bacterial genome assembly and evaluation

Abstract

With the advancement of long-read sequencing technologies and their increasing use for bacterial genomics, several methods for generating genome assemblies from error-prone long reads have been developed. These are complemented by various tools for assembly polishing using either long reads, short reads, or reference genomes. End users are therefore left with a plethora of possible combinations of programs for obtaining a final trusted assembly. Hence, there is also a need to measure the completeness and accuracy of such assemblies, for which, again, several evaluation methods implemented in various programs are available. In order to automatically run multiple genome assembly and evaluation programs at once, I developed two workflows for the workflow management system Snakemake, which provide end users with an easy-to-run solution for testing various genome assemblies from their sequencing data. Both workflows use the conda packaging system, so there is no need for manual installation of each program.