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ANI Calculation
The quickest way to calculate ANI is with FastANI. It is available as a module. To load:
module use /mod/scgc
module load fastani
FastANI instructions:
$ fastANI --help
-----------------
fastANI is a fast alignment-free implementation for computing whole-genome
Average Nucleotide Identity (ANI) between genomes
-----------------
Example usage:
$ fastANI -q genome1.fa -r genome2.fa -o output.txt
$ fastANI -q genome1.fa --rl genome_list.txt -o output.txt
Available options
-----------------
-h, --help
Print this help page
-r <value>, --ref <value>
reference genome (fasta/fastq)[.gz]
--refList <value>, --rl <value>
a file containing list of reference genome files, one genome per line
-q <value>, --query <value>
query genome (fasta/fastq)[.gz]
--ql <value>, --queryList <value>
a file containing list of query genome files, one genome per line
-k <value>, --kmer <value>
kmer size <= 16 [default : 16]
-t <value>, --threads <value>
thread count for parallel execution [default : 1]
--fragLen <value>
fragment length [default : 3,000]
--minFrag <value>
minimum matched fragments for trusting ANI [default : 50]
--visualize
output mappings for visualization, can be enabled for single genome to
single genome comparison only [disabled by default]
--matrix
also output ANI values as lower triangular matrix (format inspired from
phylip). If enabled, you should expect an output file with .matrix
extension [disabled by default]
-o <value>, --output <value> [required]
output file name
Another way to calculate ANI is by using pyani, which is a BLAST-based method. pyani is installed within SCGC's anaconda3 module, and can be run on c1 and c2.
To run pyani:
  1. 1.
    place all fasta files that you'd like to compare into a directory
  2. 2.
    Load SCGC's anaconda3 module
module use /mod/scgc
module load anaconda3
module load blast
  1. 1.
    Run pyani:
average_nucleotide_identity.py -o {outfile} -i {contig_directory} -m {choose_method, we use ANIb} --workers {threads}
Example PBS script:
#!/bin/bash
## set name of PBS job
#PBS -N pyani
## set the queue
#PBS -q scgc-route
#PBS -l walltime=96:00:00
#PBS -l mem=10G
#PBS -l ncpus=30
#PBS -j oe
#PBS -o /home/julia/out/180724_pyani.out
module unload anaconda
module load anaconda3
indir=/mnt/scgc/simon/simonsproject/contigs/
outdir = /mnt/scgc/simon/simonsproject/ani_out/
mkdir $outdir
average_nucleotide_identity.py -o ${outdir} \
-i ${indir} -m ANIb --workers 30
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