Table 1.

Description of analysis workflows. PE = paired-end; SE = single end

#	Workflow	Input	Read aligner	AV caller
1	Illumina RNAseq SE	SE fastq	bowtie2	lofreq
2	Illumina RNAseq PE	PE fastq	bwa-mem	lofreq
3	Illumina ARTIC	PE fastq	bwa-mem	lofreq
4	ONT Artic	ONT fastq/fasta	minimap2	medaka
5	Reporting	Output of any of the above workflows