PologuntingVillage
DNA concentration was determined using both NanoDrop spectrophotometers and Qubit fluorometer. Library preparations were conducted using Kits from Oxford Nanopore Technology.Nanopore sequencing was operated by MinKNOW software version 23.04.5. Basecalling was performed using Guppy version 6.5.7 with high-accuracy model [2]. The quality of FASTQ files were visualized using NanoPlot, and quality filtering was performed using NanoFilt [3][4].Reads were classified using Centrifuge classifier [5]. Bacteria and Archaea index was built using NCBI 16S RefSeq database (https://ftp.ncbi.nlm.nih.gov/refseq/TargetedLoci/). Downstream analysis and visualizations were performed using Pavian (https://github.com/fbreitwieser/pavian), Krona Tools (https://github.com/marbl/Krona), and RStudio using R version 4.2.3 (https://www.R-project.org/).