Assembly, polishing, and annotation of Salmonella DNA
Reads generated from nanopore sequencing were downsampled to generate ~100× coverage of the Salmonella Enteritidis genome using the seqtk (https://github.com/lh3/seqtk). Downsampled reads were de novoassembled using the Flye algorithm with default parameters. The assembled sequence was polished using the Unicycler_polish with the assembled contigs and the Illumina fastq reads with default parameters. The assembled Salmonella genome was annotated using the Prokka .