Table 1.

Tools used in UnCoVar depending on the type of input data (Illumina short reads or Nanopore long reads)

Stage	Step	Tool Illumina		Tool Nanopore	SARS-CoV-2 specific
Preprocessing	primer clipping	BAMClipper [30]		NoTrAmp [31]	no
	quality clipping	fastp [32]
	contamination removal	Kraken2 [33]
	Denoising	***a		Canu [34], Medaka [35]
Assembly	Assemblyb	MEGAHIT [36], metaSPAdes [37]
	scaffolding	RaGOO [38]
	polishing	BCFtools consensus [39]	Medaka consensus
Variant calling	SNV calling	freeBayes [40], DELLY [41]		Medaka variant, Longshot [42]
	SNV validation	Varlociraptor [43]
Lineage detection	read based lineage assignment	Kallisto [27]
	lineage call	Pangolin [28]			yes

^aNo denoising is performed for Illumina reads. Instead, assembly products are polished with uncertainty-aware variant calls from Varlociraptor

^bBesides the default assembly options, Trinity, Velvet, MEGAHIT-meta large/sensitive and corona-/rnaviral-/ standard SPAdes are available for use