Table 2.

Metagenomic samples used as positive controls

ID	Reconstructed Bacteria	Sequencing reads	Data type	Detected	Reference
10C	Salmonella enterica	1,017,400	Shotgun	HP, KA, MB, MI, SP	[25]
35C	Salmonella enterica	986,908	Shotgun	HP, KA, MI, SP	[25]
RK1001.C0101	Yersinia pestis	7,023,370	Shotgun	HP, KA, MI, SP	[17]
GEN_72	Yersinia pestis	7,663,408	Shotgun	HP, KA, MB, SP	[17]
549_O	Yersinia pestis	1,520,471	Shotgun	HP, KA, MI, SP	[16]
JK3031UDG	Yersinia pestis	4,059,016	Shotgun (UDG)	HP, KA, MI, SP	[16]
JK2370UDG	Yersinia pestis	52,858,027	Shotgun (UDG)	HP, KA, MB, MI, SP	[16]
RT6	Yersinia pestis	6,706,316	Shotgun (UDG)	HP, KA	[18]
1343UnTal85	Yersinia pestis	3,462,216	Shotgun	HP, KA, MB, MI, SP	[17]
6Post	Yersinia pestis	2,546,695	Shotgun	HP, KA, MB, MI, SP	[17]
KunilaII	Yersinia pestis	1,007,417	Shotgun	HP, KA, MB, MI, SP	[17]
RISE00	Yersinia pestis	6,000,000	Shotgun	HP, KA, MI, SP	[13]
RISE139	Yersinia pestis	6,000,000	Shotgun	HP, KA, MB, MI, SP	[13]
RISE386	Yersinia pestis	6,000,000	Shotgun	HP, KA, MI, SP	[13]
RISE397	Yersinia pestis	6,000,000	Shotgun	HP, KA, SP	[13]
RISE505	Yersinia pestis	6,000,000	Shotgun	HP, KA, MB, MI, SP	[13]
RISE509	Yersinia pestis	6,000,000	Shotgun	HP, KA, MB, MI, SP	[13]
RISE511	Yersinia pestis	6,000,000	Shotgun	HP, KA, SP	[13]
54	Mycobacterium tuberculosis	70,897	Shotgun	HP, KA, MI, SP	[21]
58	Mycobacterium tuberculosis	114,555	Shotgun	HP, KA, MI, SP	[21]
64	Mycobacterium tuberculosis	160,310	Shotgun	HP, KA, MB, MI, SP	[21]
54	Mycobacterium tuberculosis	5,000,000	Capture (UDG)	HP, KA, MB, MI, SP	[21]
58	Mycobacterium tuberculosis	5,000,000	Capture (UDG)	HP, KA, MB, MI, SP	[21]
64	Mycobacterium tuberculosis	5,000,000	Capture (UDG)	HP, KA, MB, MI, SP	[21]
P1P2	Helicobacter pylori	5,000,000	Capture (UDG)	HP, KA, MB, MI, SP	[27]

HP HOPS, KA KRAKEN, MB metaBIT, MI MIDAS, SP SPARSE