Table 3:

Workflow availability

Workflow	Link	History	SEEK ID
Basic workflows inspired by the Nanopolish tutorials	https://nanopore.usegalaxy.eu/u/milad/w/nanopolish-variants-tutorial	https://usegalaxy.eu/u/milad/h/nanopolish-tutorial	https://workflowhub.eu/workflows/50?version=1
Genome assembly: Flye-based WF for highly repetitive genomes [37]	https://nanopore.usegalaxy.eu/u/milad/w/ont-assembly-flye-ahrens	https://usegalaxy.eu/u/milad/h/ahrens-nanopore-gmmap	https://workflowhub.eu/workflows/51?version=1
Genome assembly: Unicycler-based WF for Klebsiella pneumoniae [51]	https://usegalaxy.eu/u/milad/h/wick-etal-nanopore	https://usegalaxy.eu/u/milad/h/wick-etal-nanopore	https://workflowhub.eu/workflows/52?version=1
Metagenomics: taxa classification	https://nanopore.usegalaxy.eu/u/milad/w/metagenomics-krakan2	https://usegalaxy.eu/u/milad/h/nanoporebeerdecodechimaytriple	https://workflowhub.eu/workflows/53?version=1

WF: workflow.