# CITATIONS

Please cite the following manuscript in your work, if you have found pyani-plus (or the older pyani) useful:

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

@Article{C5AY02550H,
author ="Pritchard, Leighton and Glover, Rachel H. and Humphris, Sonia and Elphinstone, John G. and Toth, Ian K.",
title  ="Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens",
journal  ="Anal. Methods",
year  ="2016",
volume  ="8",
issue  ="1",
pages  ="12-24",
publisher  ="The Royal Society of Chemistry",
doi  ="10.1039/C5AY02550H",
url  ="http://dx.doi.org/10.1039/C5AY02550H",
abstract  ="Soft rot Enterobacteriaceae (SRE) are bacterial plant pathogens that cause blackleg{,} wilt and soft rot diseases on a broad range of important crop and ornamental plants worldwide. These organisms (spanning the genera Erwinia{,} Pectobacterium{,} Dickeya{,} and Pantoea) cause significant economic and yield losses in the field{,} and in storage. They are transmissible through surface water{,} by trade and other movement of plant material and soil{,} and in some cases are subject to international legislative and quarantine restrictions. Effective detection and diagnosis in support of food security legislation and epidemiology is dependent on the ability to classify pathogenic isolates precisely. Diagnostics and classification are made more difficult by the influence of horizontal gene transfer on phenotype{,} and historically complex and sometimes inaccurate nomenclatural and taxonomic assignments that persist in strain collections and online sequence databases. Here{,} we briefly discuss the relationship between taxonomy{,} genotype and phenotype in the SRE{,} and their implications for diagnostic testing and legislation. We present novel whole-genome classifications of the SRE{,} illustrating inconsistencies between the established taxonomies and evidence from completely sequenced isolates. We conclude with a perspective on the future impact of widespread whole-genome sequencing and classification methods on detection and identification of bacterial plant pathogens in support of legislative and policy efforts in food security."}

When citing pyani-plus (or the older pyani) in your text, please quote the precise release version if you are using a specific release, or the specific commit hash (if you are using the 'bleeding-edge' development version), e.g.

"...using pyani-plus (v1.0.0)..."

or 

"...using pyani-plus (commit e401925)..."

This will enable precise reproduction of this part of your work by others.

Each release will have a unique DOI for Zenodo which can also be cited, see https://doi.org/10.5281/zenodo.15005805 for this.