Table 1.

Genome assemblers and polishing tools tested

Genome assembler and version	Link	Reference
Wtdbg2 v2.3	https://github.com/ruanjue/wtdbg2	[70]
Miniasm v0.3r179	https://github.com/lh3/miniasm	[39, 71]
Flye v2.3.7	https://github.com/fenderglass/Flye	[59, 72]
Canu v1.8	https://github.com/marbl/canu	[73]
SPAdes (including HybridSPAdes) v3.13.0	https://github.com/ablab/spades	[74, 75]
Skesa v2.3.0	https://github.com/ncbi/SKESA	[76]
Unicycler v0.4.7	https://github.com/rrwick/Unicycler	[77]
Assembly polishing tools
Nanopolish v0.10.2	https://github.com/jts/nanopolish	[78]
Racon v1.3.1	https://github.com/isovic/racon	[79]
Pilon v1.22	https://github.com/broadinstitute/pilon	[80]