2.3 Nanopore sequencing
On the GridION platform, sequencing libraries were constructed using the Oxford Nanopore Technologies Rapid Barcoding Sequencing kit (SQK-RBK004) and Rapid PCR Barcoding Kit (SQK-RPB004). On the PromethION platform, sequencing libraries were prepared using the Ligation Sequencing kit (SQK-LSK109) when run individually and combined with the Native Barcoding Expansion kit (EXP-NBD104 or EXP-NBD114) when multiplexed. All sequencing libraries were prepared according to the manufacturer’s protocols. Libraries were quantified and samples were either individually run or multiplexed (up to 4 samples) on MinION SpotON flow cells (R9.4.1 FLO-MIN106) when run on GridION or PromethION flow cells (FLO-PRO002) when run on PromethION. GridION runs utilized host depletion via adaptive sampling available in the MinKNOW software, which removed host reads with respect to the Sus scrofa genome (Sscrofa 11.1, accession GCF_000003025.6).