MinION-Seq of Candidatus Nitrospira kreftii enrichment
Genomic DNA was prepared for sequencing using the Ligation Sequencing Kit 1D (SQK-LSK108, Oxford Nanopore Technologies) according to the manufacturer's instructions. Adaptor-ligated DNA was cleaned by adding 0.8  volume of AMPure XP beads (Beckman Coulter Inc., Brea, CA, USA). Sequencing libraries were loaded on a SpotOn Flow Cell (FLO-MIN106 R9.4, Oxford Nanopore Technologies) using the Library Loading Beads Kit (EXP-LLB001, Oxford Nanopore Technologies) following manufacturer's specifications. Sequencing was performed on the MinION sequencing device with MinKNOW 1.7.10 software using the FLO-MIN106 450 bps protocol. Base calling of the signal data was performed using Albacore Sequencing Software 2.0.1 (Oxford Nanopore Technologies), generating 1.02 Gbp of sequencing data.