A comparison of workflows and consumable costs for various viral sequencing approaches.

The ‘Custom’ protocol refers to the modified RNA-Seq method used in this study to create larger insert fragments. Alternative methods include Amplicon-seq and hybridisation capture (SureSelect Target Enrichment for Illumina Paired-End mRNA-Seq Library Prep; version 1.1). Failure rates are determined by failure to sequence at least one amplicon (<86% of the genome). The failure rate for SureSelect is not given as it was not performed in our study. Consumable costs are list price per sample and exclude sequencing. *failure rate based on that observed with Sanger Sequencing. **estimated cost for probes only. Extra cost incurred for Agilent library preparation kit plus additional reagents recommended by Agilent. ***linear amplification during SPIA reverse transcription has not been accounted for.