Nanopore Sequencing of Pseudomonas aeruginosa

DNA extraction was performed for each of the isolated samples using the GenElute™ Bacterial Genomic DNA kit (Sigma-Aldrich). After gDNA extraction, samples were pooled to obtain samples of 400 ng gDNA to identify conserved driver mutations. Library preparation and barcoding was completed using the Rapid Barcoding Kit (Nanopore). A Nanopore MinION Sequencer was used to complete bacterial whole genome sequencing using default settings. After sequencing, quality control was performed using Epi2ME (Nanopore). Reads were trimmed using Porechop²⁹ and aligned to a reference P. aeruginosa PAO1 genome (GCF_000006765.1^{30 (link)}) using graphmap^{31 (link)}. Reads were sorted and indexed using samtools^{32 (link)}. Structural variants were identified using sniffles^{33 (link)} and SNPs were identified using BCFtools^{34 (link)}. SNPs were selected by a quality score > 20.