Data and code for “Beyond consensus sequence: a quantitative scheme for inferring transmission using deep sequencing in a bacterial transmission model”
These scripts are compatible with the following system requirements: R version 4.2.2, RStudio 2022.07.1+554, Perl v5.30.3
Description of scripts used to analyse the data
| Script | Description |
|---|---|
| Variant_calling_steps.sh | A bash file showing the steps taken to map sequence reads, call variants and generate a multi sample vcf file |
| GVCF_snp_extract_to_longtbl.pl | Perl script that takes multi-sample gvcf and extracts allelic ratio and allele calls for each sample |
| Crod_prepare_distance_tables.R | An R scripts that takes the table of allelic frequencies, a table of pairwise SNP distances and calculates changes in allelic frequencies for each pairwise comparison, the likelihood of transmission and the number of shared within host variants |
Description of data files generated in the analysis
| Data file | Description |
|---|---|
| All_snps_clean.vcf.gz | A multifile gvcf file generated using bwa, samtools, gatk, bedtools and vcfutils as described in methods |
| All_snps_summary_long_clean.csv | A table showing the allele. Frequency at each variable site for each sample in the multi-sample vcf |
| Citrobacter_distances_table.csv | A table showing the pairwise SNP distance between each pair of isolates (equivalent of a distance matrix) |