Table 1. Reference genomes for simulated read sets.

Species	Strain	Genome size (bp)	GC content	Description	MLST sequence type	Other features	GenBank assembly accession
Acinetobacter baumannii	A1	3,917,739	39.3%	Circular chromosome, one plasmid	231	Large, repetitive biofilm-associated protein gene	GCA_000830055.1
Acinetobacter baumannii	AB30	4,335,793	39.0%	Circular chromosome	758	Large, repetitive biofilm-associated protein gene	GCA_000746645.1
Escherichia coli	K-12 MG1655	4,641,652	50.8%	Circular chromosome	10		GCA_000005845.2
Escherichia coli	O25b:H4-ST131 EC958	5,249,449	50.8%	Circular chromosome, two plasmids	131		GCA_000285655.3
Klebsiella pneumoniae	30660/NJST258_1	5,540,936	57.2%	Circular chromosome, five plasmids	258		GCA_000598005.1
Klebsiella pneumoniae	MGH 78578	5,694,894	57.1%	Circular chromosome, five plasmids	38		GCA_000016305.1
Klebsiella pneumoniae	NTUH-K2044	5,472,672	57.4%	Circular chromosome, one plasmid	23		GCA_000009885.1
Mycobacterium tuberculosis	H37Rv	4,411,532	65.6%	Circular chromosome		High-copy-number PE and PPE genes	GCA_000195955.2
Saccharomyces cerevisiae	S288c	12,157,105	38.1%	16 linear chromosomes, circular mitochondrial sequence		Eukaryote	GCA_000146045.2
Shigella dysenteriae	Sd197	4,560,911	51.0%	Circular chromosome, two plasmids	146	High insertion sequence content	GCA_000012005.1
Shigella sonnei	53G	5,220,473	50.7%	Circular chromosome, four plasmids	152	High insertion sequence content	GCA_000283715.1
Streptococcus suis	BM407	2,170,808	41.0%	Circular chromosome, one plasmid	1		GCA_000026745.1