VishnuRaghuram94/SEPI

SEPI - Salmonella enterica poultry imports . Data analysis code for the study 'Genomic surveillance of Salmonella enterica Minnesota strains from poultry products imported into South Africa' # Genomic surveillance of Salmonella enterica Minnesota strains from poultry products imported into South Africa --- #### Authors: Vishnu Raghuram, Thendo Mafuna, Vignesh Ramnath, Hadrien Gourle, Josefin Blom, Kudakwashe Magwedere,Laura Carroll, Itumeleng Matle SEPI - Salmonella enterica poultry imports . Data analysis code for the study 'Genomic monitoring of Non-typhoidal Salmonella enterica serotype Minnesota associated with poultry meat imports from Brazil to South Africa' Link to raw data and intermediate files - Link to BioProject deposit - PRJNA1230142 Link to publication - ## Load libraries ### Full data table ``` r ST548_full_table % mutate(pair = ifelse(acc1 % distinct(pair, .keep_all = TRUE) %>% dplyr::select(-pair) only_ZA_snps % mutate(concordance = ifelse(`Data source.x` % reduce(left_join,by="acc") rm(list=table_names) rm(int_table) x ## Acquisition of publicly available data from Enterobase and NCBI ### Get NCBI assembly accessions ``` bash ##### Download NCBI genome summary (Was done on 18th July 2024 - file provided in 'data_tables' folder) wget "ftp.ncbi.nlm.nih.gov" head -2 assembly_summary_genbank.txt | tail -n +2 | sed 's/#//' > Salmonella_assembly_summary_genbank.txt grep "Salmonella" assembly_summary_genbank.txt >> Salmonella_assembly_summary_genbank.txt ``` ### Read Enterobase assembly table and filter samples ``` r enterobase_assembly 20000, \ =85 for genomes in Genbank only,for samples without ncbi assembly keep everything enterobase_assembly % separate_wider_delim(Species, delim = ";", names = c("Species", "Species_percent")) enterobase_assembly$Species_percent 85 & enterobase_assembly$N50>50000 & enterobase_assembly$`Contig Number(>=200 bp)` 1000 contigs # Mean genome length according to seqkit stats = 4769836 cat paths_to_all_ST548_assemblies_filtered.txt | xargs -I {} seqkit stats {} -T | grep -v "sum_len" | datamash mean 5 ``` ### Download assemblies and ins …