---
name: "fastANI"
section: "1"
platform: "linux"
package: "fastani"
version: "1.33-3+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/fastANI"
---

# fastANI(1)

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

## 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.