1263 Salmonella enterica draft genomes assembled from Bioproject PRJEB31846

We assembled 1263 Salmonella enterica draft genomes (raw data available from PRJEB31846). The dataset comprises diverse Salmonella enterica serovars collected between the years 1999 and 2019 and sequenced by the National Reference Laboratory for Salmonella on Illumina MiSeq and NextSeq technology. The data was described in more detail in 10.1128/AEM.02265-19. Data were trimmed (with fastp, version 0.19.5) and assembled (with shovil-spades, version 1.1.0) using the AQUAMIS pipeline (https://gitlab.com/bfr_bioinformatics/AQUAMIS, version v1.2.0). All samples passed basic quality checks, such as sufficient base quality, coverage depth, genome length and contig number. Furthermore, no evidence for sample contamination was detected. The assemblies are input to a validation of chewieSnake (https://gitlab.com/bfr_bioinformatics/chewieSnake). The cgMLST analysis is available in https://bfr_bioinformatics.gitlab.io/chewiesnake_publicationdata/