My paper on two Snakemake workflows for bacterial genome assembly now published in GigaByte: Snakemake workflows for long-read bacterial genome assembly and evaluation.

The first workflow, called ont-assembly-snake, is used for generating multiple genome assemblies from long-read sequencing data of a bacterial isolate. The user can freely choose from various read filtering, assembly, and polishing tools and combine them as required by creating folder names containing the order of programs to be executed.

The second workflow, called score-assemblies, is used for evaluating one or multiple genome assemblies using various programs, usually by comparison with reference assemblies, in order to help the user in deciding on a best assembly. This workflow can be run immediately after ont-assembly-snake and it outputs a report file in HTML format, which shows the key metrics from each program.