Basic Info

Using pyani to compute the genomic-level similarity of genomes

More Details

Average Nucleotide Identity (ANI) is an index used to assess the similarity of microbial genomes. It measures the relatedness between two genomes by comparing the degree of nucleotide matching in their sequences. Generally, genomes with an ANI value higher than 95%–96% are considered to belong to the same species, while those below this threshold are likely to be different species. ANI analysis is of great significance in microbial taxonomy, evolutionary studies, and genomics research, providing strong support for the accurate identification and classification of microorganisms.

What's New

pyani is a software package and Python 3 module designed to calculate ANI and related measures for whole-genome comparisons. It generates relevant graphical summary outputs and supports multiple calculation methods, including ANIm (alignment-based using MUMmer), ANIb (alignment-based using BLASTN+), and TETRA (tetranucleotide frequency analysis). Where applicable, pyani can leverage multicore systems and integrate with SGE/OGE-type job schedulers for the sequence comparisons, thereby enhancing computational efficiency.

Additional Information

Related links:

https://github.com/widdowquinn/pyani

Literature

Pritchard et al. Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens. Anal Methods, 2016,8:12-24. doi:10.1039/C5AY02550H

Goris, Johan, et al. DNA-DNA Hybridization Values and Their Relationship to Whole-Genome Sequence Similarities. International Journal of Systematic and Evolutionary Microbiology, vol. 57, no. 1, 2007, pp. 81-91. Microbiology Society, doi:10.1099/ijs.0.64483-0.