Pseudomonas aeruginosa L00 phage mining

• Find phage using Vibrant
• Search for resistance genes in vibrant outputs using RGI CARD
• Search for virulence factors in vibrant outputs using VFDB
• Blast prophage against eachother

1. Download files from Sharepoint and transfer to Quest via WinSCP

2. Create unique file name removing everything after the first period - execute command in file containing all samples

ls | cut -f1 -d. | uniq -c > samples_list.txt

See sample_list.txt

3. Use Vibrant version 1.2.0 to identify prophage and viral sequences in PA fasta files
   Bash script: vibrant_array.sh
   Output file: combined_phage.fna which contains phage identified as prophage and lytic used for downstream analysis

4. Use RGI CARD with CARD database v2.1.4 to identify Resistance Genes in phage sequences

Strict parameter produced no outputs, so parameters were loosened to retrieve all potential matches
Bash script: rgi_array.sh and rgi_loose_array.sh
Output file: rgi.txt and rgi_loose.txt

5. Use VFDB to identify virulence factors

Make a blast database using the VFDB (downloaded 8/17/2022)

module load blast/2.12.0
gunzip VFDB_setB_nt.fas.gz
makeblastdb -in VFDB_setB_nt.fasta -dbtype nucl -out VFDB_blastdb

Create bash script using awk
awk file: VFblast.awk

After creating awk file - execute the following command in the command line to create bash script for running blast

awk -f VFblast.awk sample_list.txt > VFblast_out.sh

Blast all vibrant outputs against custom database - creating pairwise and tabular outputs Bash script: VFblast.sh and VFblast_2.sh
Output file: table of query matches to virulence factor database and pairwise alignments .txt

6. Blast prophage against eachother

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