Table 1:

NanoGalaxy toolkit

Category	Tool name
De novo genome assembly	● Flye [14]● Canu [15]● Unicycler [16]● Wtdbg2 [17]● Miniasm [18]● Racon [19]● Spades [20]● Medaka (2 tools) [21]
Long-read mapping	● Minimap2 [22]
	● GraphMap (2 tools) [23]
Polishing, quality control, and pre-processing	● ont_fast5_api (4 tools) [24]● Nanopolish (3 tools) [25]● Porechop [26]● Filtlong [27]● Poretools (13 tools) [28]● Pilon [29]
Visualization	● Nanoplot [30]
	● Bandage (2 tools) [31]
	● Circos [32]
Taxonomy and metagenomics	● Kraken2 [33]
	● PlasFlow [34]
	● Staramr [35]
Methylation	● Nanopolish (1 tool) [25]
Variant calling	● Medaka (2 tools) [21]