DNA diff of phage genomes

Step 1: Install MUMmer4

Install using Conda

conda create -n mummer -c bioconda mummer4 -y
conda activate mummer

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Step 2: Prepare Genome Files

You will need two genome FASTA files:

• phageA.fna
• phageB.fna

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Step 3: Run DNAdiff

Run DNAdiff with a prefix for the output files:

dnadiff -p phageA_vs_phageB phageA.fna phageB.fna

This will generate several output files, including a summary report.

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Step 4: View the Summary Report

The main results are in the *.report file:

cat phageA_vs_phageB.report

A number of output files are created. These include :

File	Purpose
phageA_vs_phageB.report	Main summary file – identity, coverage, SNPs, indels
phageA_vs_phageB.delta	Whole-genome alignment coordinates
phageA_vs_phageB.snps	List of individual SNPs and small indels
phageA_vs_phageB.1coords	Alignment coordinates (reference → query)
phageA_vs_phageB.mcoords	Merged alignment coordinates
phageA_vs_phageB.qdiff	Regions unique to the query genome
phageA_vs_phageB.rdiff	Regions unique to the reference genome
phageA_vs_phageB.unref	Unaligned reference regions
phageA_vs_phageB.unqry	Unaligned query regions

dnadiff allows the rapid comparison of phage genomes (< 2 sec) to identify SNPs/INDELS. It works best on closely related phages.