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).