design: Double stranded cDNA was sheared using a Covaris E220 focused ultra-sonication system.  End-repair, non-templated addition of 3 poly A, adaptor ligation, pre-capture PCR, hybridisation, post-capture PCR and all post-reaction clean-up steps were performed on the Bravo NGS WorkStation Option B (Agilent Technologies) using the SureSelectXT Low Input kit (Agilent Technologies), with minor modifications to the manufacturers protocol to account for variable pathogen loads.  Quality control steps were performed using the 4200 TapeStation (Agilent Technologies).