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 .