NAME

       fastANI - Fast alignment-free computation of whole-genome Average Nucleotide Identity

DESCRIPTION

       -----------------   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]

       --minFraction <value>

              minimum fraction of genome that must be shared for trusting ANI. If  reference  and
              query genome size differ, smaller one among the two is considered. [default : 0.2]

       --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

       -v, --version

              Show version

AUTHOR

        This manpage was written by Nilesh Patra for the Debian distribution and
        can be used for any other usage of the program.