FastANI

Overview

FastANI is a program for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). It supports pairwise comparison of both complete and draft genome assemblies.

Version 1.3 is installed on the CSF.

Restrictions on use

There are no restrictions on accessing this software on the CSF. It is released under the Apache License 2.0 and all usage must adhere to that license.

Set up procedure

We now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run. See the example jobscript below for how to do this. Alternatively, you may load modulefiles on the login node and let the job inherit these settings.

Load one of the following modulefiles:

module load apps/gcc/fastani/1.3

Running the application

Please do not run fastani on the login node. Jobs should be submitted to the compute nodes via batch.

Serial batch job submission

Create a batch submission script (which will load the modulefile in the jobscript), for example:

#!/bin/bash --login
#$ -cwd             # Job will run from the current directory
                    # NO -V line - we load modulefiles in the jobscript

# Load the version you require
module load apps/gcc/fastani/1.3

# There are several ways in which FastANI can be run

# One to one
fastANI -q QUERY_GENOME -r REFERENCE_GENOME -o OUTPUT_FILE

# One to Many
fastANI -q QUERY_GENOME --rl REFERENCE_LIST -o OUTPUT_FILE

# Many to Many
fastANI --ql QUERY_LIST --rl REFERENCE_LIST -o OUTPUT_FILE

Submit the jobscript using:

qsub scriptname

where scriptname is the name of your jobscript.

Parallel batch job submission

Add the following two lines to the above jobscript before the fastANI command to make the job a parallel (multi-core job):

#$ -pe smp.pe 8                    # Number of cores, can be 2--32.
export OMP_NUM_THREADS=$NSLOTS     # Inform FastANI how many cores it can use

Further info

• FastANI website

Updates

None.