DNA of Salmonella enterica LT2
The original fluorescence image files obtained from DNBSEQ-T7 platform are transformed to short reads (Raw data) by base calling and these short reads are recorded in FASTQ (Cock et al., 2010) format. Valid sequencing data was mapped to the reference genome by BurrowsWheeler Aligner (BWA) (Li et al., 2009a) software to get the original mapping results stored in BAM format (parameter: mem -t 4 -k 32 -M). Then, the results were dislodged duplication by SAMtools (Li et al., 2009b) (parameter: rmdup) and Picard (http://broadinstitute.github.io/picard/).