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Step-by-step guide for Apple Mac OSX users

First, download necessary files

  • OAU.jar file from here.
  • USEARCH 32bit version for OSX from here.
  • Example file from here. This file contains data of an European outbreak in 2011 and related reference strains. Unzip all fasta files.

Copy all files into a directory of your choice

After copying, my directory should look like this:

Open “Terminal” program, and go the OAU directory.

Change usearch’s permission so OAU can execute it.

chmod a+x usearch9.2.64_i86osx32

Now, we are ready for run OAU.

Calculating single ANI (OrthoANIu) between two genome sequences

The following line will compare ANI between E. coli type strain (DSM 30083) and isolate C227-11.

java -jar OAU.jar -u ./usearch9.2.64_i86osx32 -f1 Example_Escherichia_coli_genome_set/Escherichia_coli_DSM_30083.fasta -f2 Example_Escherichia_coli_genome_set/Isolate_C227-11.fasta

I usually copy the output to Excel for the better formating.

Here, the result of OAU said that two genomes are related by 96.84% ANI. They are aligned side by side by 3,018,639 bp. The query (1st) genome was considered by 59.93% whereas subject (2nd) genome by 55.47%. Please note that ANI algorithms will ignore the parts of genomes that are not related or distantly related. Because this is an OrthoANI algorithm, you do not need to calculate reciprocal value.

Calculating multiple ANI values among >2 genome sequences

The following line will compare all FASTA files in a designated directory (Example_Escherichia_coli_genome_set).

java -jar OAU.jar -u ./usearch9.2.64_i86osx32 -fd Example_Escherichia_coli_genome_set

Last updated Feb 1, 2017 (JC)

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