MinION sequencing
Sequencing of 11 amplicons generating control coverage.
Lambda amplicons were amplified using Platinum Taq DNA polymerase (Thermo Scientific Invitrogen, 10966018). Primers were designed to amplify eleven 2kb regions spanning 22 kb of the lambda genome (reference strain sequence J02459.1). To prepare a mixed amplicon library, 5ul of each PCR reaction were pooled together followed by two rounds of Agencour Ampure XP purification (Beckman Coulter, A63881). This approach approximates that of Quick et al 2016. Libraries were then prepared using ONT version 6 library preparation kits (ONT, SEQ-MAP006) according to the instructions provided by ONT. Libraries were sequenced on Mk1 minIONs using FLO-MAP103 flow cells respectively. MinKNOW 0.50.2.15 was used to control the minION device using the standard 48 hour run scripts, base calling was performed using the versions of metrichor available at the time.