Table 1 List of ONT data analysis software with reliance on flowcell types or basecaller configurations

Application	Software	Flowcell type	Basecaller type	Basecaller version	Basecalling mode	Indirect
Sequence alignment	minimap2⁹	●
Error correction	HERRO³⁹	●
Variants calling	Clair3¹⁰	●	●	●	HAC/SUP ^[a]
	DeepVariant⁴⁰	●
	PEPPER⁴¹	●	●	●	SUP
	Dysgu⁴²	●
	nanomonsv⁴³	●	●	●	unspecified
	Medaka ^[b]	●	●	●	FAST, HAC, SUP
Haplotype phasing	WhatsHap⁴⁴					●^[c]
	Margin⁴¹	●	●	●	unspecified
	HapCut2⁴⁵					●^[c]
	LongPhase⁴⁶					●^[c]
Genome assembly	Flye/MetaFlye^17,47	●	●	●	HAC/SUP
	Shasta¹¹	●	●	●	HAC for Guppy 4, SUP for Guppy 6 or higher
	Canu⁴⁸	●
	wtdbg2⁴⁹					●^[d]
Genome polishing	MarginPolish¹¹	●
Genome polishing	HomoPolish⁵⁰	●	●	●	FAST, HAC, SUP

^[a] Clair3 uses the same model for the HAC and SUP modes of R9 Guppy6 data, but it uses different models for the HAC and SUP modes of R10 data.
^[b]https://github.com/nanoporetech/medaka.
^[c] These algorithms depend on the outputs of variant callers, which may be influenced by flowcell type or basecaller configuration.
^[d] Wtdbg2 depends on the sequencing error rate, which is influenced by flowcell type and basecaller configuration.
A circle mark in “Flowcell type”, “Basecaller type”, “Basecaller version”, or “Basecalling mode” indicates that the software explicitly requires this information as a mandatory input parameter. A circle mark in “Indirect” indicates that the software requires parameters derived from flowcell type or basecaller configuration, such as sequencing error rate or outputs from other software relying on these parameters. In “Basecalling mode”, “/” means the models might be used interchangeably, while “,” means each mode has a distinct associated model. If a mode is not listed, it means the current version of the software does not explicitly support it. “Unspecified” indicates a single model is provided for all modes, but it is not documented whether they can be used interchangeably. The references for the software are listed in the section References and cited in the “Software” field of the table.

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