Comparison of Illumina MiSeq and the Ion Torrent PGM and S5 platforms for whole-genome sequencing of picornaviruses and caliciviruses.

•Sequencing results and cost were compared for three library kits and benchtop sequencers.•Breadth of coverage at genome termini was influenced by library preparation.•The Ion Torrent S5 generates more high-quality reads at lower cost than the PGM.•Indels in homopolymer regions were observed in Ion Torrent S5 consensus genomes.•Illumina MiSeq was the least expensive platform for low-throughput runs.