PaSiT: a novel approach based on short-oligonucleotide frequencies for efficient bacterial identification and typing

Gleb Goussarov, Ilse Cleenwerck, Mohamed Ahmed, Natalie Leys, Pieter Monsieurs, Guillaume Tahon, Aurélien Carlier, Peter Vandamme, Rob Van Houdt

    Research outputpeer-review


    One of the most widespread methods used in taxonomy studies to distinguish between strains or taxa is the calculation of average nucleotide identity. It requires a computationally expensive alignment step and is therefore not suitable for large-scale comparisons. Short oligonucleotide-based methods do offer a faster alternative but at the expense of accuracy. Here, we aim to address this shortcoming by providing a software that implements a novel method based on short-oligonucleotide frequencies to compute inter-genomic distances.
    Original languageEnglish
    Article number964
    Pages (from-to)1-8
    Number of pages8
    StatePublished - 3 Jan 2020

    Cite this