Table 1.

Summary of the 4 Primary Hybracter Commands

Command	Input	Number of Samples	Description	Workflow Elements Included by Default (From Figure 1)
hybracter hybrid	5 column csv sample sheet specified with ‘--input’ containing:  • sample name  • long-read FASTQ path,  • estimated chromosome length  • R1 short-read FASTQ path  • R2 short-read FASTQ path	1+	Long-read first assembly followed by long then short-read polishing for multiple isolates. Snakemake implementation ensures efficient use of available resources	A, B, C, D, E, F, G, H
hybracter hybrid-single	• sample name (−s)  • long-read FASTQ path (−l)  • estimated chromosome length (−c)  • R1 short-read FASTQ path (−1)  • R2 short-read FASTQ path (−2)	1	Long-read first assembly followed by long then short-read polishing for a single isolate. Similar command line interface to Unicycler	A, B, C, D, E, F, G, H
hybracter long	3 column csv sample sheet specified with ‘--input’ containing:  • sample name  • long-read FASTQ path,  • estimated chromosome length	1+	Long-read first assembly followed by long-read polishing for multiple isolates. Snakemake implementation ensures efficient use of available resources	A (no fastp), B, C, D, E, G, H
hybracter long-single	• sample name (−s)  • long-read FASTQ path (−l)  • estimated chromosome length (−c)	1	Long-read first assembly followed by long-read polishing on a single isolate.	A (no fastp), B, C, D, E, G, H