Aligning genomes with MUMmer
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Genome Alignment

First, let’s look at our input files:

ls

We have two FASTA files:

  • H_pylori26695_Eslice.fasta: The reference strain
  • H_pyloriJ99_Eslice.fasta: The query strain

These FASTA files come from the MUMmer tutorial.

Let’s set up some variables to make our commands cleaner:

REF=H_pylori26695_Eslice.fasta QUERY=H_pyloriJ99_Eslice.fasta NAME=${REF%.fasta}_to_${QUERY%.fasta}

Let’s start by aligning two genomes using the MUMmer4 package. We use nucmer because that is MUMmer’s aligner for nucleotide sequences (“nuc”), i.e. DNA or RNA sequences, and here we are aligning DNA.

nucmer --prefix $NAME $REF $QUERY
(This might take a minute)

This will create a delta file containing the alignments. The --prefix option sets the prefix for output files.

Let’s look at the first few lines of the delta file:

head $NAME.delta

The delta file format is not very human-readable, so in the next step we’ll convert it to a more useful format.

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