title: Escherichia coli whole Genome sequencing and assembly
design: The Illumina NextSeq 2000 platform performed whole genome sequencing of one bacterial DNA sample, generating paired-end reads with a read length of 151 bp. We used FastQC analysis (Andrews, 2010) to check the quality of the data, and then we used Fastp v0.23.4 with the parameters --average_qual 20 and --length_required 35 to trim the adapter and filter the quality (Chen et al., 2018). We used Unicycler v0.5.0 to put together a new genome from the trimmed reads, setting a minimum contig length of 200 bp (Wick et al., 2017). Finally, we conducted genome annotation using Prokka v1.14.5, adhering to genetic code 11 (Seemann et al., 2014).