Shotgun metagenomics of activated sludge
Library preparation of the extracted DNA was performed using the Ligation Sequencing Kit V12 (Oxford Nanopore Technologies Ltd). The NEBNext Companion Module for Oxford Nanopore Technologies Ligation Sequencing (New England BioLabs Inc.) and UltraPureTM BSA (50 mg/mL) (Thermo Fisher Scientific) were additionally used for the DNA repair and end-prep and the flow cell priming steps. All steps were performed as instructed by the manufacturer. All resuspension steps were performed by flicking the tube. MinION R9.4 version flow cells (Oxford Nanopore) were loaded with the DNA and sample was sequenced in accurate mode (260 bps) for 72h. The reads were already filtered and trimmed.