Table 4. Open in new tab Query...

Table 4.

Query performance.

Data	Algorithm	Type^d	Speed^e (kb/s)	RAM (GB)
SR+^a	ropebwt3^f	MEM31	1758.5	10.6
		MEM51	1907.5	10.6
		SW10	84.1	15.2
	MONI^g	MEM–	453.2	68.4
		extend	348.2	68.4
	Movi	PML	5894.0	47.6
	metagraph	PA+	<0.1	65.3
	fulgor	PA	2717.5	5.1
LR+^b	ropebwt3	MEM31	1695.9	10.5
		MEM51	1793.9	10.5
		SW25	82.7	15.6
	MONI	MEM–	413.6	68.4
	Movi	PML	16204.9	47.6
	metagraph	PA+	<0.1	65.3
	fulgor	PA	2491.6	5.1
LR−^c	ropebwt3	MEM31	1365.0	10.4
		MEM51	3051.6	10.4
		SW25	58.2	17.9
	MONI	MEM–	186.8	68.4
	Movi	PML	8490.9	47.6
	metagraph	PA+	1119.3	65.3
	fulgor	PA	4240.8	5.1

Data	Algorithm	Type^d	Speed^e (kb/s)	RAM (GB)
SR+^a	ropebwt3^f	MEM31	1758.5	10.6
		MEM51	1907.5	10.6
		SW10	84.1	15.2
	MONI^g	MEM–	453.2	68.4
		extend	348.2	68.4
	Movi	PML	5894.0	47.6
	metagraph	PA+	<0.1	65.3
	fulgor	PA	2717.5	5.1
LR+^b	ropebwt3	MEM31	1695.9	10.5
		MEM51	1793.9	10.5
		SW25	82.7	15.6
	MONI	MEM–	413.6	68.4
	Movi	PML	16204.9	47.6
	metagraph	PA+	<0.1	65.3
	fulgor	PA	2491.6	5.1
LR−^c	ropebwt3	MEM31	1365.0	10.4
		MEM51	3051.6	10.4
		SW25	58.2	17.9
	MONI	MEM–	186.8	68.4
	Movi	PML	8490.9	47.6
	metagraph	PA+	1119.3	65.3
	fulgor	PA	4240.8	5.1

First 1 million 125 bp human short reads from SRR3099549.

First 10 000 human PacBio HiFi reads from SRR26545347.

First 10 000 metagenomic PacBio HiFi reads from DRR290133.

MEMx: super-maximal exact matches (SMEMs) of x bp or longer with counts; MEM–: SMEM without counts; extend: Smith-Waterman extension from the longest SMEM; PML: pseudo-matching length; PA: pseudo-alignment; PA+: pseudo-alignment with contig names; SWy: BWA-SW with bandwidth y.

Kilobases processed per CPU second. Index loading time excluded.

Index in the binary fermi format.

The MONI index includes both strands. We modified MONI such that extension is performed on the forward query strand only.

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