title: Nanopore sequencing of SARS-CoV-2 positive sample
design: Robotic extraction was implemented on a Tecan EVO-200 system keeping all the steps, buffers, and RNA elution volumes similar to manual protocol (Supplementary Material 1A & 1D). The robot configuration and script are described in https://github.com/strubelab/roboRNA. One step R3T qRT-PCR was performed with the US CDC 2019-nCoV assay (nCoV_N1, nCoV_N2 and RNase P, (IDT Cat. No. 10006770)). The reaction was composed of 5 L of 2X R3T qRT-PCR reaction buffer mix, 0.5 L of R3T qRT-PCR enzyme mix, 0.5 L of each probe/primer mix (nCoV_N1, nCoV_N2 or rNase P), 4 L of eluted RNA. The reaction was performed in a CFX384 Touch Real-Time PCR System (BIO-RAD) using the following program: 55 C 30 min, 94 C 2 min, 45 cycles of 94 C 15 sec, 58 C 30 sec, and 68 C 1 min; 68 C 5 min. TaqPath 1-Step RT-qPCR Master Mix (ThermoFisher Scientific, A15299) was used following the suppliers instructions.