title: Nanopore sequencing of humanT stool
design: The DNA was extracted from each sample using the ZymoBIOMICS DNA extraction protocol (Zymo Research, USA). The DNA purity was quantified using a Nanodrop Spectrophotometer (NanoDrop Technology, USA) by measuring the A260/280 and A260/230 ratios. The DNA concentration was quantified using a Qubit 3.0 Fluorometer (Invitrogen, USA). The integrity of the extracted DNA was evaluated with agarose gel electrophoresis (Thermo Scientific, USA). Extracted DNA samples were stored at 4 C for 24 hours before sequencing. We used a MinION (Oxford Nanopore Technologies [ONT], USA) device with a ligation sequencing kit (SQK-LSK108, ONT, USA) and followed the manufacturer's 1D Genomic DNA sequencing protocol for library preparation.  Briefly, for each sample, 1100 ng of genomic DNA was repaired using the NEBNext FFPE repair mix (New England Biolabs [NEB], USA), according to manufacturer recommendations, and the DNA was subsequently purified using AMPureXP beads (Beckman Coulter, USA). End-repair of DNA fragments was then performed using the NEBNext Ultra II End Prep/dA-tailing module (NEB, USA), and DNA was subsequently purified again using AMPure XP beads. Next, ligation of motor protein-complexed AMX adapter to genomic DNA ends was carried out using the NEB Blunt/TA ligase Master Mix (NEB, USA). A final round of AMPure XP purification was then performed before the DNA library was eluted and loaded onto a flow cell for sequencing. Sequencing of the genomic DNA was performed on a single R9.5/FLO-MIN107 flow cell (ONT, USA) on a MinION Mk1B  (ONT, USA) for 48 hours.