This repository holds scripts used for a masters project which involved the assembly of 11 strains of Escherichia coli and Escherichia marmotae, and the investigation of their virulence and resistance gene content.

The scripts in this repository were used for the following:

1. assembly_pipeline.sh - This bash script was used to trim raw paired-end reads in .fastq.gz files and assemble trimmed reads using the shovill pipeline. It also runs prokka for annotation of the assembly, quast for assemby quality statistics and ABRicate and AMRFinder for the identification of resistance, virulence and plasmid genes from assemblies.

2. Project_Heatmaps.Rmd This is an R markdown document containing the Copy_number_matrix() function used in R to format ABRicate and AMRFinder outputs into copy number matrices. It also contains the commands where these matrices were used as input for the pheatmap() function to create the heatmaps available as supplementary figures in the manuscript. It requires names_total.csv and heatmaps_metadata.csv to correctly name strains in the matrices and provide metadata for heatmaps.

3. Plasmid_contig_genes.Rmd This is an R markdown document containing the Plasmid_contents() function used in R to find virulence or resistance genes on the same sequence as a plasmid gene using the ABRicate PlasmidFinder data and another ABRicate or AMRFinder dataset. It also contains the commands used to get the output that was used for supplememtary table 2 of the manuscript. It requires names_total.csv to correctly name strains.

4. database_amr.sh was a bash script used to run abricate and AMRFinder for .gff, .fna and .faa files associated with genomes downloaded on NCBI, and database_prokka.sh was a bash script used to re-annotate the E. marmotae genomes downloaded from NCBI to get the input .gff files used for Roary.

Outside of these scripts, the following commands were used to run other software:

1. Running Roary: singularity run ../scripts/roary.img roary -p 8 roary/*gff

2. Running Parsnp: singularity run ../scripts/parsnp.img parsnp -r ../phylogeny/assembled/HT073016-2_annotated.fna -d ../phylogeny/assembled/