FastANI is a software tool for computation of whole-genome ANI (Average Nucleotide Identity) which is a measure of nucleotide-level genomic similarity between two complete or draft microbial genomes assemblies. Its procedure follows an alignment-free workflow by using MashMap which makes it much faster than alignment-based methods. The provided results for genomes with more than 80% similarity are essentially identical to their related alignment-based ANI figures.

Button16 Important.png Important: FastANI requires Linux or Windows with installed Windows Subsystem For Linux.

In addition, for using FastANI on Windows with installed WSL, the library libgomp1 must be installed, too. This can be done by executing the following line in WSL:
sudo apt-get update; sudo apt-get install libgomp1

Tools Menu Genome Similarity (FastANI)

Genome Similarity (FastANI) Dialog

The menu function Tools | Genome Utilities | Genome Similarity (FastANI) can be used to calculate similarity of read files (FASTQ). One or multiple files can be selected as References and Queries to be compared pairwise. The number of Threads that should be used for processing can be specified. When the dialog is confirmed, FastANI is started to compare all references against all queries. No ANI output is reported for a genome pair if the ANI value is below 80%.

The resulting table is shown in new dialog and contains the following columns:

  • Name contains the query file name without extension.
  • Query is the full file name of the query.
  • Reference shows the complete name of the reference file.
  • ANI value is the result figure for query-reference pair.
  • Aligned as Orthologous Matches and Sequence Fragments as shared and total orthologous gene pairs fragments.