[OAU] Manual

[EzEditor2] Tutorial
05/15/2017
[OAU] Mac OSX
05/15/2017

[OAU] Manual

Contents

  • About
  • Installation
  • Options
  • Single ANI calculation example
  • Multiple ANI calculation example
  • Contact


About

  • OAU is a command line tool for calculating OrthoANI values using the USEARCH algorithm. OAU can be used to calculate a single OrthoANI value between two genome sequence files (fasta format), or to calculate OrthoANI values between all unique pairings of genome sequence files in a specified directory. Although this command line tool can be used with all operating systems that run Java, we recommend using a Unix-like operating system (most commonly Linux and OSX) for optimal results.

Installation

  • OAU is a standalone program that doesn’t require installation. However, it does have dependencies. Your system will need to be able to run Java (most likely installed by default), and you’ll also need to have the USEARCH program downloaded. Please put OAU.jar in a directory of your choosing and run it from the command line. You can download OAU from EzBioCloud here.
    You can download USEARCH from the author’s download page. For bacterial genomes, 32 bit version is sufficient.
  • For a step-by-step tutorial for Apple Mac OSX users, visit here.

Options

OAU has the following options:

-f1        Absolute path of first input fasta file
-f2       Absolute path of second input fasta file
-fd       Absolute path of directory with multiple fasta files
-fmt    Output format
-o         Absolute path of output result file
-t          Absolute path of temporary directory
-u         Absolute path of USEARCH program

The required options are -u and either -fd or both -f1 and -f2.

If -fd is given, then -f1 and -f2 are not required. If -fd is not given, then both -f1 and -f2 are required.

If you want to calculate a single OrthoANI value between two genomes of your choosing, please use -f1 to specify the first genome sequence file and -f2 to specify the second genome sequence file.

If you want to calculate OrthoANI values between multiple genomes, please place your genome sequence files in a single directory and use -fd to specify this directory when running OAU.

Output format can be specified by using the -fmt option, which can take one of two arguments: list or matrix. This is an optional parameter, and the default output format will be in a list format.

If an output file is not specified using -o, the program will print results to stdout.

You can provide a temporary directory to store intermediate files using -t. Intermediate files will be created in the specified directory while the program is running (or in /tmp/ if no arguments provided), and will be deleted after the program is done running.

USEARCH path is a required parameter, and you must download the USEARCH program separately, as the author of the algorithm provides his own license agreement for using the algorithm.


Single ANI calculation example

java -jar OAU.jar -u /path/to/usearch -f1 /path/to/first_genome_file -f2 /path/to/second_genome_file -o /path/to/desired_output_file

Multiple ANI calculation example

java -jar OAU.jar -u /path/to/usearch -fd /path/to/fasta_files_directory -o /path/to/desired_output_file


Contact

Last modified on January 30, 2017 (SJK)

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