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

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

fastANI 1.32                                       March 2021                                         FASTANI(1)

-----------------  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

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