Table 4. Resource usage metrics for the execution of all pipelines using strain KpBSB53 data, as measured automatically by Nextflow.

For bacannot, only the most time and memory-consuming tasks are shown.

Pipeline	Software	Task	Duration (min)	% of pipeline duration	Memory (Gb)
ngs-preprocess	fastp	short-reads preprocessing	7	7.6	2.7
ngs-preprocess	porechop	long-reads preprocessing	70	76.1	4.4
ngs-preprocess	nanopack	filter and quality check	15	16.3	2.1
MpGAP	Flye	assembly	48	5.4	11.3
MpGAP	medaka	long-reads polishing	28	3.18	9.5
MpGAP	pilon	short-reads polishing	625	70.8	10.6
MpGAP	QUAST & Busco	quality check	182	20.6	10.2
MpGAP	MultiQC	reporting	0.2	0.02	0.7
bacannot	Prokka	gene annotation	16	43.2	1
bacannot	Platon	plasmid detection	2	5.4	3.6