Metagenomic identification and characterisation of Salmonella enterica from faecal samples

This study tested whether or not metagenomics can be used to identify and characterise Salmonella enterica from faecal metagenomes. The metagenomes were downloaded from ENA/SRA project PRJEB21259, trimmed with fastp v0.23.4 and the host reads were removed with hostile v0.1.0. The metagenomes were compared to those from paediatric healthy controls obtained from SRA project PRJEB22032 (DOI: 10.1093/infdis/jiab398), which were pre-processed in the same way. The trimmed, host-removed reads from both datasets are deposited here.